last updated: Tuesday, 05-Aug-2025 16:14:07 EDT
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
Versions: 2.3.2; 3.0.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
amber
==============================================================================
Description: A package of molecular simulation programs which includes
source code and demos.
Versions: 22; 24
License: Campus Agreement
Categories: Computational Chemistry
==============================================================================
Ames Stereo Pipeline
==============================================================================
Description: The NASA Ames Stereo Pipeline is a suite of automated
Versions: 3.4.0
License: https://go.dev/LICENSE?m=text
Categories: NASA, stereogrammetry
==============================================================================
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: 2023.03; 2024.02; 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; 24.2; 25.1
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; 0.17.1; 0.17.2; 0.18.0
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: Armadillo is a high quality linear algebra library (matrix
maths) for the C++ language
Versions: 11.4.2; 12.6.7; 14.6.1
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
==============================================================================
aspera-cli
==============================================================================
Description: The Aspera CLI client for the Fast and Secure Protocol (FASP).
Versions: 3.7.7
License: N/A
Categories: N/A
==============================================================================
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; 3.5.0
License: GNU GPL
Categories: Bioinformatics, Sequencing, gene prediction
==============================================================================
autoconf
==============================================================================
Description: Autoconf -- system configuration part of autotools
Versions: 2.72
License: N/A
Categories: N/A
==============================================================================
automake
==============================================================================
Description: Automake -- make file builder part of autotools
Versions: 1.16.5
License: N/A
Categories: N/A
==============================================================================
aws-cli
==============================================================================
Description: AWS command line interface
Versions: False
License: https://aws.amazon.com/terms/
Categories: Amazon, AWS, utility
==============================================================================
AzCopy
==============================================================================
Description: CLI utility for storage management.
Versions: 10.28.1
License: NA
Categories: utility, storage
==============================================================================
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: 1.21; 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; 4.3.6
License: GPLv2
Categories: Bioinformatics
==============================================================================
bcl2fastq2
==============================================================================
Description: The bcl2fastq2 Conversion Software converts base call (BCL)
files from a sequencing run into FASTQ files.
Versions: 2.20.0.422
License: N/A
Categories: N/A
==============================================================================
bdftopcf
==============================================================================
Description: bdftopcf is a font compiler for the X server and font server.
Fonts in Portable Compiled Format can be read by any
architecture, although the file is structured to allow one
particular architecture to read them directly without
reformatting. This allows fast reading on the appropriate
machine, but the files are still portable (but read more
slowly) on other machines.
Versions: 1.1.1
License: N/A
Categories: N/A
==============================================================================
beast1
==============================================================================
Description: BEAST is a cross-platform program for Bayesian analysis of
molecular sequences using MCMC.
Versions: 1.10.4
License: N/A
Categories: N/A
==============================================================================
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; 2.31.1
License: N/A
Categories: N/A
==============================================================================
berkeley-db
==============================================================================
Description: Oracle Berkeley DB
Versions: 18.1.40
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
==============================================================================
bison
==============================================================================
Description: Bison is a general-purpose parser generator that converts an
annotated context-free grammar into a deterministic LR or
generalized LR (GLR) parser employing LALR(1) parser tables.
Versions: 3.8.2
License: N/A
Categories: N/A
==============================================================================
blast-plus
==============================================================================
Description: Basic Local Alignment Search Tool.
Versions: 2.16.0; 2.12.0
License: NA
Categories: Bioinformatics
==============================================================================
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; 1.88.0
License: http://www.boost.org/users/license.html
Categories: Programming, C++, library
==============================================================================
bowtie
==============================================================================
Description: Bowtie is an ultrafast, memory-efficient short read aligner
for short DNA sequences (reads) from next-gen sequencers.
Versions: 1.3.0
License: N/A
Categories: N/A
==============================================================================
bowtie2
==============================================================================
Description: Bowtie 2 is an ultrafast and memory-efficient tool for
aligning sequencing reads to long reference sequences
Versions: 2.4.1; 2.4.2
License: N/A
Categories: N/A
==============================================================================
BPCells
==============================================================================
Description: R libraries necessary for BPCells
Versions: 0.3.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
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
==============================================================================
bzip2
==============================================================================
Description: bzip2 is a freely available, patent free high-quality data
compressor. It typically compresses files to within 10% to 15%
of the best available techniques (the PPM family of
statistical compressors), whilst being around twice as fast at
compression and six times faster at decompression.
Versions: 1.0.8
License: N/A
Categories: N/A
==============================================================================
ca-certificates-mozilla
==============================================================================
Description: The Mozilla CA certificate store in PEM format
Versions: 2023-05-30
License: N/A
Categories: N/A
==============================================================================
Cactus
==============================================================================
Description: Cactus is a reference-free whole-genome alignment program, as
well as a pangenome graph construction toolkit.
Versions: 2.9.8
License:
https://github.com/ComparativeGenomicsToolkit/cactus/blob/mast
er/LICENSE.txt
Categories: Bioinformatics, Sequencing, Alignment
==============================================================================
Caiman
==============================================================================
Description: Caiman is a software package for analysis of calcium imaging
data.
Versions: 1.12.1
License: N/A
Categories: Neuroscience, data analysis, imaging
==============================================================================
canu
==============================================================================
Description: A single molecule sequence assembler for genomes large and
small.
Versions: 2.2
License: N/A
Categories: N/A
==============================================================================
cap3
==============================================================================
Description: CAP3 is DNA Sequence Assembly Program
Versions: 2015-02-11
License: N/A
Categories: N/A
==============================================================================
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; 2.4.1
License: N/A
Categories: cli, climate
==============================================================================
cellbender
==============================================================================
Description: CellBender is a software package for eliminating technical
artifacts from high-throughput single-cell RNA sequencing
(scRNA-seq) data.
Versions: 0.3.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
cellpose
==============================================================================
Description: cellpose is an anatomical segmentation algorithm written in
Python 3.
Versions: 2.1.1; 3.0.10
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; 9.0.0; 9.0.1; 9.0.a
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
==============================================================================
Chemkin Chemkin
==============================================================================
Description: Chemkin is a software tool for modeling and simulating complex
chemical reactions and reaction kinetics. Chemkin-Pro module
Versions: 22.2; 25.1
License: Academic Research
Categories: Chemical reaction modeling, Simulation
==============================================================================
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: 2022.1.2; 14.0.6
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; 4.0.3
License: https://cmake.org/licensing/
Categories: Utility, programming, compiler
==============================================================================
cmake
==============================================================================
Description: A cross-platform, open-source build system. CMake is a family
of tools designed to build, test and package software.
Versions: 3.30.5
License: N/A
Categories: N/A
==============================================================================
CMTK
==============================================================================
Description: A software toolkit for computational morphometry of biomedical
images, Computational Morphometry Toolkit (CMTK) comprises a
set of command line tools and a back-end general-purpose
library for processing and I/O.
Versions: 3.3.1
License: GNU GPL v1.3 or later
Categories: Neuroimaging, Morphometry,
==============================================================================
code-server
==============================================================================
Description: Run VS Code on any machine anywhere and access it in the
browser.
Versions: 4.100.2; 4.8.3; 4.91.0
License: MIT
Categories: file management, software development, scripting, IDE.
==============================================================================
COMSOL
==============================================================================
Description: COMSOL is multiphysics simulation software.
Versions: 6.0; 6.1; 6.2; 6.3
License:
https:/www.comsol.com/documentation/6.0/COMSOL_SoftwareLicense
Agreement.pdf
Categories: Multiphysics, simulation
==============================================================================
connect-proxy
==============================================================================
Description: connect-proxy open connection over SOCKS4/5 proxies
Versions: 1.105
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
Convert3D
==============================================================================
Description: Convert3D
Versions: 1.0.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
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
==============================================================================
CTFFind
==============================================================================
Description: CTFFind (a program for finding the CTFs of electron
micrographs)
Versions: 4.1.14
License: Janelia Research Campus Software Copyright 1.1
Categories: cryo-em
==============================================================================
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; 12.6.3; 12.8.1
License: http://docs.nvidia.com/cuda/eula/index.html
Categories: CUDA, gpu, library, programming
==============================================================================
cudnn
==============================================================================
Description: cuDNN libraries.
Versions: 10.2-v8.3.1; 11.2-v8.1.1; 11.3-v8.2.1; 11.5-v8.3.1;
11.6-v8.4.1; 11.7-v8.7.0; 11.8-v8.7.0; 12.1-v8.9.0;
12.3-v8.9.6; 12.6-v9.3.0; 12.6-v9.6.0; 12.8-v9.10.0
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; 12.6.3; 12.8.1
License: http://docs.nvidia.com/cuda/eula
Categories: CUDA, gpu, library, programming, Profiler
==============================================================================
curl
==============================================================================
Description: cURL is an open source command line tool and library for
transferring data with URL syntax
Versions: 8.10.1
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
dcmb551
==============================================================================
Description: A collection of Java based utilities for DCMB 551 class
Versions: 1.0
License: N/A
Categories: Bioinformatics
==============================================================================
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
==============================================================================
DeepLabCutLive
==============================================================================
Description: Contains a DeepLabCut inference pipeline for real-time
applications
Versions: 1.04
License: GPLv3
Categories: Bioinformatics
==============================================================================
deepvariant
==============================================================================
Description: DeepVariant is a deep learning-based variant caller
Versions: 1.9.0
License: GPLv2
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; 2025
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
==============================================================================
DESeq2
==============================================================================
Description: Estimate variance-mean dependence in count data from high-
throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution.
Versions: 1.46.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
DIAMOND
==============================================================================
Description: Accelerated BLAST compatible local sequence aligner
Versions: 2.1.8.162
License: GPL-3.0 License
Categories: Bioinformatics
==============================================================================
diffutils
==============================================================================
Description: GNU Diffutils is a package of several programs related to
finding differences between files.
Versions: 3.10
License: N/A
Categories: N/A
==============================================================================
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; 0.8.1; 0.8.2; 0.9.0;
0.9.1; 1.0.2
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; 7.4.12
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
==============================================================================
DRGN-AI
==============================================================================
Description: DRGN-AI is a neural network-based algorithm for ab initio
heterogeneous cryo-EM reconstruction
Versions: 1.0.1
License: GPL-3.0
Categories: cryo-em
==============================================================================
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
==============================================================================
elfutils
==============================================================================
Description: elfutils is a collection of various binary tools such as eu-
objdump, eu-readelf, and other utilities that allow you to
inspect and manipulate ELF files. Refer to Table 5.Tools
Included in elfutils for Red Hat Developer for a complete list
of binary tools that are distributed with the Red Hat
Developer Toolset version of elfutils.
Versions: 0.191
License: N/A
Categories: N/A
==============================================================================
EnTAP
==============================================================================
Description: EnTAP is an eukaryotic non-model annotation pipeline.
Versions: 1.0.1; 2.0.0
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
==============================================================================
expat
==============================================================================
Description: Expat is an XML parser library written in C.
Versions: 2.6.4
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
FCS-GX
==============================================================================
Description: Detects contamination from foreign organisms in genome
sequences
Versions: 0.5.5
License: United States Copyright Act
Categories: Bioinformatics
==============================================================================
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; 2024.1
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; 7.1.0
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; 1.5.4
License: GPLv2
Categories: Bioinformatics
==============================================================================
filtlong
==============================================================================
Description: a tool for filtering long reads by quality
Versions: 0.2.1
License: GPLv2
Categories: Bioinformatics
==============================================================================
findutils
==============================================================================
Description: The GNU Find Utilities are the basic directory searching
utilities of the GNU operating system.
Versions: 4.9.0
License: N/A
Categories: N/A
==============================================================================
flex
==============================================================================
Description: Flex is a tool for generating scanners.
Versions: 2.6.3
License: N/A
Categories: N/A
==============================================================================
Flye
==============================================================================
Description: Flye is a de novo assembler for single-molecule sequencing
reads, such as those produced by PacBio and Oxford Nanopore
Technologies. It is designed for a wide range of datasets,
from small bacterial projects to large mammalian-scale
assemblies. The package represents a complete pipeline: it
takes raw PacBio / ONT reads as input and outputs polished
contigs. Flye also has a special mode for metagenome assembly.
Currently, Flye will produce collapsed assemblies of diploid
genomes, represented by a single mosaic haplotype. To recover
two phased haplotypes consider applying HapDup after the
assembly.
Versions: 2.9.2; 2.9.5
License: BSD-3 License:
https://github.com/fenderglass/Flye/blob/flye/LICENSE
Categories: Bioinformatics
==============================================================================
font-util
==============================================================================
Description: X.Org font package creation/installation utilities and fonts.
Versions: 1.4.1
License: N/A
Categories: N/A
==============================================================================
fontsproto
==============================================================================
Description: X Fonts Extension.
Versions: 2.1.3
License: N/A
Categories: N/A
==============================================================================
FragPipe
==============================================================================
Description: A complte proteomics pipeline with the MSFragger search engine
at heart
Versions: 22.0
License: https://github.com/Nesvilab/FragPipe?tab=License-1-ov-
file#readme
Categories: proteomics
==============================================================================
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
==============================================================================
freetype
==============================================================================
Description: FreeType is a freely available software library to render
fonts. It is written in C, designed to be small, efficient,
highly customizable, and portable while capable of producing
high-quality output (glyph images) of most vector and bitmap
font formats.
Versions: 2.13.2
License: N/A
Categories: N/A
==============================================================================
fribidi
==============================================================================
Description: GNU FriBidi: The Free Implementation of the Unicode
Bidirectional Algorithm.
Versions: 1.0.12
License: N/A
Categories: N/A
==============================================================================
FSL
==============================================================================
Description: FSL suite of MRI neuroimaging tools.
Versions: 6.0.1; 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; 14.1.0; 15.1.0; 8.2.0
License: GPL
Categories: Compiler, programming, development
==============================================================================
gcc-runtime
==============================================================================
Description: Package for GCC compiler runtime libraries
Versions: 13.2.0
License: N/A
Categories: N/A
==============================================================================
GDAL
==============================================================================
Description: GDAL is a translator library for raster and vector geospatial
data formats.
Versions: 3.5.1; 3.8.3; 3.11.3
License: https://gdal.org/license.html
Categories: GIS, geospatial, raster, vector, graphics
==============================================================================
gdbm
==============================================================================
Description: GNU dbm (or GDBM, for short) is a library of database
functions that use extensible hashing and work similar to the
standard UNIX dbm. These routines are provided to a programmer
needing to create and manipulate a hashed database.
Versions: 1.23
License: N/A
Categories: N/A
==============================================================================
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; 3.13.1
License: GNU LGPL v2.1
Categories: GIS, Geometry, OSGeo
==============================================================================
gettext
==============================================================================
Description: GNU internationalization (i18n) and localization (l10n)
library.
Versions: 0.22.5
License: N/A
Categories: N/A
==============================================================================
git
==============================================================================
Description: Git version control software
Versions: 2.39.1
License: GPL version 2
Categories: Utility, development, version control
==============================================================================
git-annex
==============================================================================
Description: Manage large files with git, without storing the file contents
in git
Versions: 10.20220928
License: AGPL version 3.0
Categories: Utility, development, version control, file management
==============================================================================
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
==============================================================================
glibc
==============================================================================
Description: The GNU C Library provides many of the low-level components
used directly by programs written in the C or C++ languages.
Versions: 2.28
License: N/A
Categories: N/A
==============================================================================
glmGamPoi
==============================================================================
Description: R libraries necessary for glmGamPoi
Versions: 1.18.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
globus-cli
==============================================================================
Description: The CLI provides an interface to Globus services from the
shell, and is suited to both interactive and simple scripting
use cases.
Versions: 3.19.0; 3.29.0; 3.30.1; 3.32.0; 3.33.0; 3.35.0; 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
==============================================================================
glpk
==============================================================================
Description: The GLPK (GNU Linear Programming Kit) package is intended for
solving large-scale linear programming (LP), mixed integer
programming (MIP), and other related problems. It is a set of
routines written in ANSI C and organized in the form of a
callable library.
Versions: 5.0
License: N/A
Categories: N/A
==============================================================================
gmake
==============================================================================
Description: GNU Make is a tool which controls the generation of
executables and other non-source files of a program from the
program's source files.
Versions: 4.4.1
License: N/A
Categories: N/A
==============================================================================
gmp
==============================================================================
Description: GMP is a free library for arbitrary precision arithmetic,
operating on signed integers, rational numbers, and floating-
point numbers.
Versions: 6.3.0
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
gnina
==============================================================================
Description: A deep learning framework for molecular docking
Versions: 1.3
License: Apache-2.0
https://github.com/gnina/gnina/blob/master/LICENSE.APACHE
Categories: molecular docking, deep learning, cheminformatics
==============================================================================
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
==============================================================================
gperf
==============================================================================
Description: GNU gperf is a perfect hash function generator. For a given
list of strings, it produces a hash function and hash table,
in form of C or C++ code, for looking up a value depending on
the input string. The hash function is perfect, which means
that the hash table has no collisions, and the hash table
lookup needs a single string comparison only.
Versions: 3.1
License: N/A
Categories: N/A
==============================================================================
graphite2
==============================================================================
Description: Graphite is a system that can be used to create 'smart fonts'
capable of displaying writing systems with various complex
behaviors. A smart font contains not only letter shapes but
also additional instructions indicating how to combine and
position the letters in complex ways.
Versions: 1.3.14
License: N/A
Categories: N/A
==============================================================================
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; 2025.2
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; 11.0.3; 12.0.1; 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; 1.12.1
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
==============================================================================
Hifiasm
==============================================================================
Description: Hifiasm delivers high-quality telomere-to-telomere assemblies.
Versions: 0.19.9
License: MIT License
Categories: Bioinformatics
==============================================================================
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
==============================================================================
hmmer
==============================================================================
Description: HMMER is used for searching sequence databases for sequence
homologs, and for making sequence alignments. It implements
methods using probabilistic models called profile hidden
Markov models (profile HMMs).
Versions: 3.4
License: N/A
Categories: N/A
==============================================================================
homer
==============================================================================
Description: Software for motif discovery and next generation sequencing
analysis
Versions: 4.11.1
License: N/A
Categories: N/A
==============================================================================
HPC compilers
==============================================================================
Description: Compiler suite.
Versions: 22.3; 24.7
License: https://docs.nvidia.com/hpc-sdk/eula/hpc-sdk-ea-eula.pdf
Categories: Compiler, development, debugger, profiler
==============================================================================
htslib
==============================================================================
Description: C library for high-throughput sequencing data formats.
Versions: 1.12; 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: 9.0
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
==============================================================================
IMOD
==============================================================================
Description: IMOD is a set of image processing, modeling and display
programs used for tomographic reconstruction and for 3D
reconstruction of EM serial sections and optical sections
Versions: 4.12.57
License: N/A
Categories: electron microscopy, electron tomography, cryo-em, cryo-et
==============================================================================
impi
==============================================================================
Description: Intel MPI runtime
Versions: 2021.5.1
License: GPL
Categories: MPI, MPICH, programming
==============================================================================
impute2
==============================================================================
Description: IMPUTE2 is a genotype imputation and haplotype phasing program
based on ideas from Howie et al. 2009.
Versions: 2.3.2
License: N/A
Categories: N/A
==============================================================================
inputproto
==============================================================================
Description: X Input Extension.
Versions: 2.3.2
License: N/A
Categories: N/A
==============================================================================
Intel
==============================================================================
Description: Intel compiler suite.
Versions: 2022.1.2
License: None provided
Categories: Library, Development, Core
==============================================================================
Intel VTune Profiler
==============================================================================
Description: Intel VTune Profiler is a performance analysis tool for
analyzing code execution and identifying performance
bottlenecks in applications developed for Intel architectures.
Versions: 2022.1.0
License: None Provided
Categories: performance analysis, profiling, software optimization
==============================================================================
itk
==============================================================================
Description: 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
==============================================================================
itksnap
==============================================================================
Description: ITK-SNAP is a free, open-source, multi-platform software
application used to segment structures in 3D and 4D biomedical
images..
Versions: 4.0.2
License: GPLv3
Categories: Bioinformatics
==============================================================================
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; 4.3.2
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
==============================================================================
Jax
==============================================================================
Description: Array computation library for accelerators using python
Versions: 0.4.30
License: Apache-2.0 license
Categories: Programming, numerical library, accelerators, python
==============================================================================
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; 1.11.4; 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
==============================================================================
kbproto
==============================================================================
Description: X Keyboard Extension.
Versions: 1.0.7
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
krb5
==============================================================================
Description: Network authentication protocol
Versions: 1.21.3
License: N/A
Categories: N/A
==============================================================================
LabGym
==============================================================================
Description: Image and Video processing software for identifying social
behaviors in multi-individual interactions
Versions: 2.5.5; 2.8.0; 2.9.0
License: GPL-3.0
Categories: Image Segmentation, Machine Learning
==============================================================================
LAMMPS
==============================================================================
Description: LAMMPS is a classical molecular dynamics code that models an
ensemble of particles.
Versions: 02Aug2023; 23Jun2022; 27May21; 29Aug2024; 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; 3.12.1
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
==============================================================================
Leptonica Leptonica
==============================================================================
Description: Image processing and image analysis library Image processing
and image analysis library
Versions: 1.82.0
License: http://www.leptonica.org/about-the-license.html
http://www.leptonica.org/about-the-license.html
Categories: image processing, image analysis, OCR image processing, image
analysis, OCR
==============================================================================
LFTP
==============================================================================
Description: File transfer program
Versions: 4.9.2
License: GNU General Public License
Categories: file transfer, transfer
==============================================================================
libbsd
==============================================================================
Description: This library provides useful functions commonly found on BSD
systems, and lacking on others like GNU systems, thus making
it easier to port projects with strong BSD origins, without
needing to embed the same code over and over again on each
project.
Versions: 0.12.2
License: N/A
Categories: N/A
==============================================================================
libffi
==============================================================================
Description: The libffi library provides a portable, high level programming
interface to various calling conventions. This allows a
programmer to call any function specified by a call interface
description at run time.
Versions: 3.4.6
License: N/A
Categories: N/A
==============================================================================
libfontenc
==============================================================================
Description: libfontenc - font encoding library.
Versions: 1.1.8
License: N/A
Categories: N/A
==============================================================================
libgd
==============================================================================
Description: GD graphics library
Versions: 2.3.3
License: https://github.com/libgd/libgd?tab=License-1-ov-file#readme
Categories: multimedia
==============================================================================
libgit2
==============================================================================
Description: A cross-platform, linkable library implementation of Git that
you can use in your application.
Versions: 1.8.4
License: GPLv2
Categories: Git
==============================================================================
libice
==============================================================================
Description: libICE - Inter-Client Exchange Library.
Versions: 1.1.1
License: N/A
Categories: N/A
==============================================================================
libiconv
==============================================================================
Description: GNU libiconv provides an implementation of the iconv()
function and the iconv program for character set conversion.
Versions: 1.17
License: N/A
Categories: N/A
==============================================================================
libidn2
==============================================================================
Description: Libidn2 is a free software implementation of IDNA2008,
Punycode and TR46. Its purpose is to encode and decode
internationalized domain names.
Versions: 2.3.7
License: N/A
Categories: N/A
==============================================================================
libjpeg-turbo
==============================================================================
Description: libjpeg-turbo is a fork of the original IJG libjpeg which uses
SIMD to accelerate baseline JPEG compression and
decompression.
Versions: 3.0.3
License: N/A
Categories: N/A
==============================================================================
libmd
==============================================================================
Description: This library provides message digest functions found on BSD
systems either on their libc (NetBSD, OpenBSD) or libmd
(FreeBSD, DragonflyBSD, macOS, Solaris) libraries and lacking
on others like GNU systems.
Versions: 1.0.4
License: N/A
Categories: N/A
==============================================================================
libpng
==============================================================================
Description: libpng is a library for working with PNG image files.
Versions: 1.5.30; 1.6.39
License: N/A
Categories: Graphics, Imaging
==============================================================================
libpthread-stubs
==============================================================================
Description: The libpthread-stubs package provides weak aliases for pthread
functions not provided in libc or otherwise available by
default.
Versions: 0.5
License: N/A
Categories: N/A
==============================================================================
libsigsegv
==============================================================================
Description: GNU libsigsegv is a library for handling page faults in user
mode.
Versions: 2.14
License: N/A
Categories: N/A
==============================================================================
libsm
==============================================================================
Description: libSM - X Session Management Library.
Versions: 1.2.4
License: N/A
Categories: N/A
==============================================================================
libsodium
==============================================================================
Description: encryption library
Versions: 1.0.20
License: ISC License
Categories: library
==============================================================================
libtiff
==============================================================================
Description: LibTIFF - Tag Image File Format (TIFF) Library and Utilities.
Versions: 4.7.0
License: N/A
Categories: N/A
==============================================================================
libtirpc
==============================================================================
Description: Libtirpc is a port of Suns Transport-Independent RPC library
to Linux.
Versions: 1.3.3
License: N/A
Categories: N/A
==============================================================================
libtool
==============================================================================
Description: libtool -- library building part of autotools.
Versions: 2.4.7
License: N/A
Categories: N/A
==============================================================================
libunistring
==============================================================================
Description: This library provides functions for manipulating Unicode
strings and for manipulating C strings according to the
Unicode standard.
Versions: 1.2
License: N/A
Categories: N/A
==============================================================================
libxau
==============================================================================
Description: The libXau package contains a library implementing the X11
Authorization Protocol. This is useful for restricting client
access to the display.
Versions: 1.0.11
License: N/A
Categories: N/A
==============================================================================
libxcrypt
==============================================================================
Description: libxcrypt is a modern library for one-way hashing of
passwords.
Versions: 4.4.35
License: N/A
Categories: N/A
==============================================================================
libxdmcp
==============================================================================
Description: libXdmcp - X Display Manager Control Protocol library.
Versions: 1.1.5
License: N/A
Categories: N/A
==============================================================================
libxfont
==============================================================================
Description: libXfont provides the core of the legacy X11 font system,
handling the index files (fonts.dir, fonts.alias,
fonts.scale), the various font file formats, and rasterizing
them. It is used by the X servers, the X Font Server (xfs),
and some font utilities (bdftopcf for instance), but should
not be used by normal X11 clients. X11 clients access fonts
via either the new API's in libXft, or the legacy API's in
libX11.
Versions: 1.5.4
License: N/A
Categories: N/A
==============================================================================
libxml2
==============================================================================
Description: Libxml2 is the XML C parser and toolkit developed for the
Gnome project (but usable outside of the Gnome platform), it
is free software available under the MIT License.
Versions: 2.13.4
License: N/A
Categories: N/A
==============================================================================
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; 24.0.4
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
==============================================================================
m4
==============================================================================
Description: GNU M4 is an implementation of the traditional Unix macro
processor.
Versions: 1.4.19
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
mamba
==============================================================================
Description: Python Data Science Distribution
Versions: 3.10; 3.11; 3.12
License: https://github.com/mamba-org/mamba?tab=BSD-3-Clause-1-ov-
file#readme
Categories: Python, Programming, Scripting, numpy, scipy, matplotlib,
ipython, jupyter, mamba
==============================================================================
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
==============================================================================
MaSuRCA
==============================================================================
Description: The MaSuRCA assembler combines the benefits of deBruijn graph
and Overlap-Layout-Consensus assembly approaches.
Versions: 4.1.0
License: GPL-3.0 License
Categories: Bioinformatics
==============================================================================
Mathematica
==============================================================================
Description: Mathematical and technical computing package.
Versions: 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; R2024b
License: N/A
Categories: Mathematics, programming, simulation
==============================================================================
Matplotlib
==============================================================================
Description: Visualization with Python.
Versions: 3.5.3
License: https://github.com/matplotlib/matplotlib/tree/main/LICENSE
Categories: Programming, python, visualization, graph, image
==============================================================================
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
==============================================================================
mkfontdir
==============================================================================
Description: mkfontdir creates the fonts.dir files needed by the legacy X
server core font system. The current implementation is a
simple wrapper script around the mkfontscale program, which
must be built and installed first.
Versions: 1.0.7
License: N/A
Categories: N/A
==============================================================================
mkfontscale
==============================================================================
Description: mkfontscale creates the fonts.scale and fonts.dir index files
used by the legacy X11 font system.
Versions: 1.2.3
License: N/A
Categories: N/A
==============================================================================
MKL
==============================================================================
Description: Intel optimized BLAS/LAPACK libraries, also including FFT and
other mathematical and statistical routines.
Versions: 2018.0.4; 2023.2.1
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
==============================================================================
MotionCor2
==============================================================================
Description: MotionCor2 is a multi-GPU movie alignment program.
Versions: 1.4.7
License: Free for academic and/or non-profit use
Categories: cryo-em
==============================================================================
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
==============================================================================
multiqc
==============================================================================
Description: Aggregate bioinformatics results across many samples into a
single report
Versions: 1.22.2
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
==============================================================================
mysql
==============================================================================
Description: open-source relational database client
Versions: 9.3.0; 8.0.35
License: https://github.com/mysql
Categories: Database, relational
==============================================================================
mzmine
==============================================================================
Description: an open-source software for mass-spectrometry data processing
Versions: 4.2.0
License: N/A
Categories: Bioinformatics
==============================================================================
N/A
==============================================================================
Description: N/A
Versions: 2025.05.0; 1.18.0; 5.0.7; 5.0.8
License: N/A
Categories: N/A
==============================================================================
nanoplot
==============================================================================
Description: Plotting tool for long read sequencing data and alignments.
Versions: 1.42.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
nasm
==============================================================================
Description: NASM (Netwide Assembler) is an 80x86 assembler designed for
portability and modularity. It includes a disassembler as
well.
Versions: 2.16.03
License: N/A
Categories: N/A
==============================================================================
Natural Bond Orbital (NBO)
==============================================================================
Description: Computational chemistry program for the analysis of many-
electron molecular wavefunctions.
Versions: 7.0
License: (c) Copyright 1996-2018 Board of Regents of the University of
Wisconsin System on behalf of the Theoretical Chemistry
Institute. All rights reserved.
Categories: Computational Chemistry, Quantum Chemistry, simulation.
==============================================================================
ncftp
==============================================================================
Description: NcFTP Client is a set of application programs implementing the
File Transfer Protocol.
Versions: 3.2.6
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
ncurses
==============================================================================
Description: The ncurses (new curses) library is a free software emulation
of curses in System V Release 4.0, and more. It uses terminfo
format, supports pads and color and multiple highlights and
forms characters and function-key mapping, and has all the
other SYSV-curses enhancements over BSD curses.
Versions: 6.5
License: N/A
Categories: N/A
==============================================================================
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; 4.9.3
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; 4.6.2
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; 8.2.7; 8.2.3
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
==============================================================================
NextDenovo
==============================================================================
Description: AboutFast and accurate de novo assembler for long reads
Versions: 2.5.2
License: GPL-3.0 License
Categories: Bioinformatics
==============================================================================
nextflow
==============================================================================
Description: Data-driven computational pipelines.
Versions: 24.10.0
License: N/A
Categories: N/A
==============================================================================
ngc-cli
==============================================================================
Description: NVIDIA NGC CLI is a command-line interface tool for managing
Docker containers in the NVIDIA NGC Registry.
Versions: 3.54.0
License: GNU GPL V3
Categories: netCDF, visual browser, utility
==============================================================================
nghttp2
==============================================================================
Description: nghttp2 is an implementation of HTTP/2 and its header
compression algorithm HPACK in C.
Versions: 1.63.0
License: N/A
Categories: N/A
==============================================================================
node.js
==============================================================================
Description: JavaScript runtime environment
Versions: 22.14.0
License: https://github.com/nodejs/node/tree/main?tab=License-1-ov-
file#readme
Categories: runtime
==============================================================================
nsight-compute
==============================================================================
Description: NVIDIA Nsight Compute - interactive profiler for CUDA kernels.
Versions: 2025.2
License: https://docs.nvidia.com/nsight-compute/License.html
Categories: CUDA, gpu, profiling, performance
==============================================================================
NumPy
==============================================================================
Description: Numerical libraries for use within Python.
Versions: 1.22.3
License: https://github.com/numpy/numpy
Categories: Programming, numerical library, BLAS, LAPACK, python
==============================================================================
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
==============================================================================
Ollama
==============================================================================
Description: Lightweight platform for deploying and fine-tuning large
language models (LLMs)
Versions: ollama
License: See official documentation
Categories: AI/ML
==============================================================================
openblas
==============================================================================
Description: BLAS provides standard interfaces for linear algebra,
including vector-vector operations, matrix-vector operations,
and matrix-matrix operations.
Versions: 0.3.19; 0.3.23; 0.3.30; 0.3.28
License: https://opensource.org/licenses/BSD-3-Clause
Categories: Programming, C++, library
==============================================================================
OpenFOAM
==============================================================================
Description: OpenFOAM is a free, open source CFD software.
Versions: 10; v2112; v2212; v2406
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; 21.0.1
License: GPLv2 with linking exception
Categories: Java, programming
==============================================================================
openjdk
==============================================================================
Description: The free and opensource java implementation
Versions: 17.0.11_9
License: N/A
Categories: N/A
==============================================================================
OpenMPI
==============================================================================
Description: OpenMPI implementation of the MPI protocol
Versions: 4.1.3; 4.1.4; 4.1.6; 5.0.3; 4.1.7; 3.1.6
License: https://www.open-mpi.org/community/license.php
Categories: Utility, Development, Core
==============================================================================
openmpi
==============================================================================
Description: An open source Message Passing Interface implementation.
Versions: 5.0.3
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
openssl
==============================================================================
Description: OpenSSL is an open source project that provides a robust,
commercial-grade, and full-featured toolkit for the Transport
Layer Security (TLS) and Secure Sockets Layer (SSL) protocols.
It is also a general-purpose cryptography library.
Versions: 3.4.0
License: N/A
Categories: N/A
==============================================================================
OpenStudio
==============================================================================
Description: Energy modeling software
Versions: 3.7.0
License: https://github.com/NREL/OpenStudio/?tab=License-1-ov-
file#readme
Categories: Energy modeling
==============================================================================
orca
==============================================================================
Description: A powerful and versatile quantum chemistry software package
Versions: 4.2.1; 5.0.3; 6.0.1
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; 5.12.1
License: http://www.paraview.org/license/
Categories: Visualization, data analysis,
==============================================================================
pcre2
==============================================================================
Description: The PCRE2 package contains Perl Compatible Regular Expression
libraries. These are useful for implementing regular
expression pattern matching using the same syntax and
semantics as Perl 5.
Versions: 10.44
License: N/A
Categories: N/A
==============================================================================
perl
==============================================================================
Description: Perl 5 is a highly capable, feature-rich programming language
with over 27 years of development.
Versions: 5.40.0
License: N/A
Categories: N/A
==============================================================================
perl-modules
==============================================================================
Description: Perl addin modules for use with Perl version 5.26.3.
Versions: 1.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
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
==============================================================================
pigz
==============================================================================
Description: A parallel implementation of gzip for modern multi-processor,
multi-core machines.
Versions: 2.8
License: N/A
Categories: N/A
==============================================================================
pkgconf
==============================================================================
Description: pkgconf is a program which helps to configure compiler and
linker flags for development frameworks. It is similar to pkg-
config from freedesktop.org, providing additional
functionality while also maintaining compatibility.
Versions: 2.2.0
License: N/A
Categories: N/A
==============================================================================
plink
==============================================================================
Description: PLINK a whole genome association analysis toolset.
Versions: 1.9; 2.0; 2.3a; 2.3a3; 2.3dev; 2.4a4
License: GPLv3
Categories: Bioinformatics
==============================================================================
pNetCDF
==============================================================================
Description: Libraries for creating and manipulating Parallel NetCDF files.
Versions: 1.13.0
License: https://github.com/Parallel-
NetCDF/PnetCDF/blob/master/COPYRIGHT
Categories: Library, Development, Core
==============================================================================
Poetry
==============================================================================
Description: Python packaging and dependency management.
Versions: 1.6.1
License: https://github.com/python-poetry/poetry
Categories: Programming, dependency management, python
==============================================================================
polypolish
==============================================================================
Description: a tool for polishing genome assemblies with short reads
Versions: 0.6.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
presto
==============================================================================
Description: R libraries necessary for presto
Versions: 1.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
Prodigal
==============================================================================
Description: Prodigal (Prokaryotic Dynamic Programming Genefinding
Algorithm) is a microbial (bacterial and archaeal) gene
finding program.
Versions: 2.6.3
License: GPL3
Categories: Bioinformatics gene genefinding genetics
==============================================================================
PROJ
==============================================================================
Description: PROJ is a generic coordinate transformation software.
Versions: 9.0.0; 9.3.1; 9.4.1
License: MIT
Categories: GIS, Library
==============================================================================
prokka
==============================================================================
Description: Prokka: rapid prokaryotic genome annotation
Versions: 1.14.5
License: GPLv2
Categories: Bioinformatics
==============================================================================
py-azure-cli
==============================================================================
Description: Microsoft Azure Command-Line Tools.
Versions: 2.9.1
License: N/A
Categories: N/A
==============================================================================
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; 3.13.2; 3.9.12
License: https://docs.python.org/3/license.html
Categories: Programming, language
==============================================================================
PyTorch
==============================================================================
Description: Python tensor library for deep learning.
Versions: 1.12.1; 2.0.1
License: https://pytorch.org/
Categories: Programming, python, machine learning, tensor, GPU
==============================================================================
qiime
==============================================================================
Description: QIIME. (canonically pronounced chime) stands for Quantitative
Insights Into Microbial Ecology.
Versions: 1.8.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
Qt5
==============================================================================
Description: Development Tools Qt is designed for developing applications
and user interfaces
Versions: 5.12.11
License: GNU Lesser General Public License v. 3 (“LGPL”)
Categories: Development
==============================================================================
qt6-devel
==============================================================================
Description: Development package for the Qt6 cross-platform application
framework.
Versions: 6.9.1
License: N/A
Categories: Development, GUI, Multimedia
==============================================================================
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; 7.3.1
License: http://www2.mmm.ucar.edu/wrf/users/public.html
Categories: electronic structure, materials modeling, ab initio quantum
chemistry
==============================================================================
quast
==============================================================================
Description: QUality ASsessment Tool
Versions: 5.2.0
License: GNU GPL v2
Categories: Bioinformatics
==============================================================================
QuPath
==============================================================================
Description: QuPath is open source software for bioimage analysis
Versions: 0.7.0
License: GPLv3
Categories: Bioinformatics
==============================================================================
R
==============================================================================
Description: R environment for statistical computing and graphics
Versions: 4.2.0; 4.3.1; 4.3.2; 4.4.0; 4.4.3
License: GPL, https://www.r-project.org/Licenses/
Categories: Statistics, graphics, big data, data science
==============================================================================
r-seurat
==============================================================================
Description: Tools for Single Cell Genomics.
Versions: 5.1.0; 4.1.1
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
RAxML-NG
==============================================================================
Description: RAxML Next Generation
Versions: 1.2.2
License: GPLv2
Categories: Bioinformatics
==============================================================================
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
==============================================================================
readline
==============================================================================
Description: The GNU Readline library provides a set of functions for use
by applications that allow users to edit command lines as they
are typed in. Both Emacs and vi editing modes are available.
The Readline library includes additional functions to maintain
a list of previously-entered command lines, to recall and
perhaps reedit those lines, and perform csh-like history
expansion on previous commands.
Versions: 8.2
License: N/A
Categories: N/A
==============================================================================
RELION
==============================================================================
Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce
rely-on)
Versions: 3.1.3; 4.0.0; 4.0.2; 5.0.0
License: GPL-v2
Categories: cryo-em, cryo-et
==============================================================================
renderproto
==============================================================================
Description: X Rendering Extension.
Versions: 0.11.1
License: N/A
Categories: N/A
==============================================================================
RepeatMasker
==============================================================================
Description: A program that screens DNA sequences.
Versions: 4.1.9
License: OSIv2.1
Categories: Bioinformatics
==============================================================================
Rgeospatial
==============================================================================
Description: A collection of R geospatial libraries
Versions: 2022-08-18; 2023-04-25; 2023-07-01; 2024-01-15; 2024-05-11;
2025-04-21
License: GPL, https://www.r-project.org/Licenses/
Categories: Statistics, graphics, big data, data science, geospatial,
geography, spatial, map
==============================================================================
Rgiotto
==============================================================================
Description: R libraries necessary for Giotto
Versions: 1.1.0; 4.2.0
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; 1.3.7
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; 4.4.3
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; 3.14
License: GPLv2
Categories: Bioinformatics
==============================================================================
RosettaDDG
==============================================================================
Description: RosettaDDGPrediction is a Python package to run Rosetta-based
protocols
Versions: 3.12
License: GPLv2
Categories: Bioinformatics
==============================================================================
RpowsimR
==============================================================================
Description: R libraries necessary for powsimR
Versions: 1.2.5
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-R4.4.0; 5.0.1; 5.3.0-R4.4.3
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; 2024.04.1
License: AGPL v3
Categories: Statistics, graphics, big data, data science, IDE
==============================================================================
Rtidyverse
==============================================================================
Description: R Tidyverse environment for statistical computing and graphics
Versions: 4.2.0; 4.3.1; 4.3.2; 4.4.0; 4.4.3
License: GPL, https://www.r-project.org/Licenses/
Categories: Statistics, graphics, big data, data science, tidyverse
==============================================================================
ruby
==============================================================================
Description: A dynamic, open source programming language with a focus on
simplicity and productivity
Versions: 3.3.3
License: GPLv3
Categories: Bioinformatics
==============================================================================
Rust
==============================================================================
Description: general purpose programming language
Versions: 1.81.0
License: MIT, Apache 2.0
Categories: development, programming, languages
==============================================================================
Rutils-BFX
==============================================================================
Description: R libraries necessary for the BFX core
Versions: 1.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
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: 10.4; 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: 1.21; 1.13; 1.9
License: GPLv2
Categories: Bioinformatics
==============================================================================
SAS
==============================================================================
Description: SAS statistical system software.
Versions: 9.4-TS1M7; 9.4-TS1M8
License: Not available
Categories: Statistics, econometrics
==============================================================================
scCATCH
==============================================================================
Description: R libraries necessary for scCATCH
Versions: 3.2.2
License: GPLv2
Categories: Bioinformatics
==============================================================================
schrodinger
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact drugdiscovery@umich.edu]
Schrodinger Suite
Versions: 2024-2; 2025-2
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
==============================================================================
scrnsaverproto
==============================================================================
Description: MIT Screen Saver Extension.
Versions: 1.2.2
License: N/A
Categories: N/A
==============================================================================
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: 4.1.3; 4.3.1
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
==============================================================================
Snakemake
==============================================================================
Description: Workflow management system for reproducible and scalable data
analyses.
Versions: 9.5.1
License: https://github.com/snakemake/snakemake/blob/master/LICENSE.md
Categories: Workflow, pipeline, automation, bioinformatics, python
==============================================================================
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; 3.0.1; 3.1.1; 3.1.2; 3.1.3;
4.0.1
License: GPLv2
Categories: Bioinformatics
==============================================================================
Spack Package Manager
==============================================================================
Description: A flexible package manager supporting multiple versions,
configurations, platforms, and compilers.
Versions: 0.21; 0.23
License: Apache-2.0
Categories: Software Installation, compiling, package manager
==============================================================================
SPAdes
==============================================================================
Description: SPAdes package provides pipelines for DNA assembly of isolates
and single-cell bacteria
Versions: 4.0.0
License: https://github.com/ablab/spades?tab=License-1-ov-file
Categories: Bioinformatics
==============================================================================
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
==============================================================================
sqlite
==============================================================================
Description: SQLite is a C-language library that implements a small, fast,
self-contained, high-reliability, full-featured, SQL database
engine.
Versions: 3.46.0
License: N/A
Categories: N/A
==============================================================================
sratoolkit
==============================================================================
Description: A collection of tools and libraries for using data in the
INSDC Sequence Read Archives.
Versions: 3.1.1; 2.10.9
License: GPL
Categories: Bioinformatics
==============================================================================
Stacks
==============================================================================
Description: Stacks is a software pipeline for building loci from short-
read sequences, such as those generated on the Illumina
platform
Versions: 2.65
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; 19.02.013-R8; 19.02.013
License: Academic Research
Categories: CFD
==============================================================================
Stata/MP
==============================================================================
Description: Statistical analysis software.
Versions: 17; 18; 19
License: http://www.stata.com/order/end-user-license-agreement/
Categories: Statistics, econometrics
==============================================================================
Stata/SE
==============================================================================
Description: Statistical analysis software.
Versions: 17; 18; 19
License: http://www.stata.com/order/end-user-license-agreement/
Categories: Statistics, econometrics
==============================================================================
stringtie
==============================================================================
Description: Transcript assembly and quantification for RNA-Seq
Versions: 2.2.1; 2.1.7
License: GPLv2
Categories: Bioinformatics
==============================================================================
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
==============================================================================
tar
==============================================================================
Description: GNU Tar provides the ability to create tar archives, as well
as various other kinds of manipulation.
Versions: 1.34
License: N/A
Categories: N/A
==============================================================================
TBB
==============================================================================
Description: Intel Thread Building Blocks.
Versions: 2022.1.2
License: https://software.intel.com/en-us/articles/end-user-license-
agreement
Categories: Library, development, core, thread
==============================================================================
tcl
==============================================================================
Description: Tcl (Tool Command Language) is a very powerful but easy to
learn dynamic programming language, suitable for a very wide
range of uses, including web and desktop applications,
networking, administration, testing and many more. Open source
and business-friendly, Tcl is a mature yet evolving language
that is truly cross platform, easily deployed and highly
extensible.
Versions: 8.6.12
License: N/A
Categories: N/A
==============================================================================
Tecplot 360 & Tecplot Chorus
==============================================================================
Description: Plotting and visualization software that gives full control
over 2-D and 3-D plot parameters.
Versions: 2022r1
License: N/A
Categories: plotting, visualization
==============================================================================
TensorFlow
==============================================================================
Description: Machine learning platform for use within Python.
Versions: 2.7.0
License: Apache License 2.0
Categories: Programming, machine learning library, python
==============================================================================
TensorRT
==============================================================================
Description: An SDK for high-performance deep learning inference.
Versions: 11.8-v8.6.1
License: Apache License 2.0
Categories: Programming, Machine Learning, Tensorflow, Inference
==============================================================================
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
==============================================================================
texinfo
==============================================================================
Description: Texinfo is the official documentation format of the GNU
project.
Versions: 7.1
License: N/A
Categories: N/A
==============================================================================
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
==============================================================================
trilinos
==============================================================================
Description: Libraries for robust computation of automatic diffusion,
multi-level preconditioners, incomplete factorization,
nonlinear methods, time integration methods, etc.
Versions: 16.0.0; 16.1.0
License: https://trilinos.github.io/license.html
Categories: Library, Development, Core, Multi-Physics, Computation,
Mathematics, Math
==============================================================================
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
==============================================================================
util-linux-uuid
==============================================================================
Description: Util-linux is a suite of essential utilities for any Linux
system.
Versions: 2.40.2
License: N/A
Categories: N/A
==============================================================================
util-macros
==============================================================================
Description: This is a set of autoconf macros used by the configure.ac
scripts in other Xorg modular packages, and is needed to
generate new versions of their configure scripts with
autoconf.
Versions: 1.20.1
License: N/A
Categories: N/A
==============================================================================
uv
==============================================================================
Description: An extremely fast Python package and project manager, written
in Rust.
Versions: 0.5.1
License: https://github.com/astral-sh/uv/blob/main/LICENSE-
APACHE,https://github.com/astral-sh/uv/blob/main/LICENSE-MIT
Categories: package manager
==============================================================================
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
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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
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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
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VESTA
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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
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VisIt
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Description: VisIt data analysis and visualization application.
Versions: 3.3.1
License: N/A
Categories: Visualization, data analysis
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VLC
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Description: VLC media player
Versions: 3.0.9
License: GPLv2
Categories: Bioinformatics
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vtk
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Description: data visualization
Versions: 9.3.1
License: BSD
Categories: Graphics
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Wannier90
==============================================================================
Description: Maximally-localised Wannier functions (MLWFs) and Wannier90
Versions: 1.2; 2.1
License: http://www.wannier.org
Categories: MLWFs, electronic structure code
==============================================================================
which
==============================================================================
Description: GNU which - is a utility that is used to find which executable
(or alias or shell function) is executed when entered on the
shell prompt.
Versions: 2.21
License: N/A
Categories: N/A
==============================================================================
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
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xcb-devel
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Description: xcb development libraries and headers
Versions: 0.4.1
License: MIT License
Categories: Libraries, Headers
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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
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xeniumranger
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Description: a set of software applications for analyzing and visualizing
in situ gene expression data produced by the Xenium Analyzer
Versions: 3.0.1
License: GPLv2
Categories: Bioinformatics
==============================================================================
xextproto
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Description: X Protocol Extensions.
Versions: 7.3.0
License: N/A
Categories: N/A
==============================================================================
xproto
==============================================================================
Description: X Window System Core Protocol.
Versions: 7.0.31
License: N/A
Categories: N/A
==============================================================================
xtrans
==============================================================================
Description: xtrans is a library of code that is shared among various X
packages to handle network protocol transport in a modular
fashion, allowing a single place to add new transport types.
It is used by the X server, libX11, libICE, the X font server,
and related components.
Versions: 1.5.2
License: N/A
Categories: N/A
==============================================================================
xz
==============================================================================
Description: XZ Utils is free general-purpose data compression software
with high compression ratio. XZ Utils were written for POSIX-
like systems, but also work on some not-so-POSIX systems. XZ
Utils are the successor to LZMA Utils.
Versions: 5.4.6
License: N/A
Categories: N/A
==============================================================================
Yasm
==============================================================================
Description: Yasm assembler.
Versions: 1.3.0; 2.15.05
License: https://github.com/yasm/yasm/blob/master/BSD.txt
Categories: assembler, programming
==============================================================================
zip
==============================================================================
Description: Zip is a compression and file packaging/archive utility.
Versions: 3.0
License: N/A
Categories: N/A
==============================================================================
zlib-ng
==============================================================================
Description: zlib replacement with optimizations for next generation
systems.
Versions: 2.2.1
License: N/A
Categories: N/A
==============================================================================
zstd
==============================================================================
Description: Zstandard, or zstd as short version, is a fast lossless
compression algorithm, targeting real-time compression
scenarios at zlib-level and better compression ratios.
Versions: 1.5.6
License: N/A
Categories: N/A
==============================================================================