last updated: Friday, 19-Apr-2024 11:00:05 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 v2 Versions: 2.3.2 License: GPLv2 Categories: Bioinformatics ============================================================================== amber ============================================================================== Description: A package of molecular simulation programs which includes source code and demos. Versions: 22 License: Campus Agreement Categories: Computational Chemistry ============================================================================== AMPL ============================================================================== Description: AMPL algebraic modeling language. Versions: 20220703 License: http://ampl.com/buy-ampl-terms-and-conditions/ Categories: Optimization, linear programming, algebraic modeling ============================================================================== AMRfinder ============================================================================== Description: This software is designed to find acquired antimicrobial resistance genes and point mutations Versions: 3.12.8 License: 'United States Government Work' under the terms of the United States Copyright Act Categories: Bioinformatics ============================================================================== Anaconda3 ============================================================================== Description: Python Data Science Distribution Versions: 2023.03; 2021.11 License: https://www.anaconda.com/eula-anaconda-individual-edition Categories: Python, Programming, Scripting, numpy, scipy, matplotlib, ipython, jupyter ============================================================================== angsd ============================================================================== Description: Angsd is a program for analysing NGS data. Versions: 0.935 License: N/A Categories: N/A ============================================================================== annotSV ============================================================================== Description: Annotation and Ranking of Human Structural Variations Versions: 2.2 License: GPLv2 Categories: Bioinformatics ============================================================================== annovar ============================================================================== Description: ANNOVAR is an efficient software tool to functionally annotate genetic variants detected from diverse genomes Versions: 9.2019 License: GPLv2 Categories: Bioinformatics ============================================================================== ANSYS ============================================================================== Description: ANSYS is a finite element simulation tool for multiphysics simulations. Versions: 21.2; 22.2 License: Academic Research Categories: CFD, FEM, finite element, multiphysics ============================================================================== ANSYS EM ============================================================================== Description: ANSYS EM: HFSS and Maxwell Versions: 21.2; 22.2 License: Academic Research Categories: EM, CEM, HFSS, Maxwell ============================================================================== ANTs ============================================================================== Description: ANTs MRI image registration program Versions: 2.4.1 License: ANTs is Apache License 2.0 Categories: image processing, image registration, fMRI, neuroimaging ============================================================================== Anvi'o ============================================================================== Description: Anvi'o is an analysis and visualization platform for 'omics data. Versions: 7.1; 7 License: GPL3 Categories: bioinformatics, genomics, visualization ============================================================================== arb ============================================================================== Description: The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. Versions: 7.0 License: GPLv2 Categories: Bioinformatics ============================================================================== archivetar ============================================================================== Description: Parallel archive manipulation tool Versions: 0.15.6; 0.16.0; 0.17.0 License: https://github.com/brockpalen/archivetar/blob/master/LICENSE Categories: Utility ============================================================================== ArchR ============================================================================== Description: R libraries necessary for ArchR Versions: 1.0.2 License: GPLv2 Categories: Bioinformatics ============================================================================== ARM Forge ============================================================================== Description: Parallel debugging and profiling tools, DDT and MAP. Versions: 21.1.3 License: Not available Categories: Programming, profiler, debugger, performance ============================================================================== armadillo ============================================================================== Description: rmadillo is a high quality linear algebra library (matrix maths) for the C++ language Versions: 11.4.2; 12.6.7 License: http://www.netlib.org/lapack/LICENSE.txt Categories: Libraries ============================================================================== Asgard ============================================================================== Description: R libraries necessary for Asgard Versions: 1.0.0 License: GPLv2 Categories: Bioinformatics ============================================================================== atactk ============================================================================== Description: A toolkit for working with ATAC-seq data. Versions: 0.1.9 License: GPLv2 Categories: Bioinformatics ============================================================================== Augustus ============================================================================== Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Versions: 3.3 License: GNU GPL Categories: Bioinformatics, Sequencing, gene prediction ============================================================================== aws-cli ============================================================================== Description: AWS command line interface Versions: False License: https://aws.amazon.com/terms/ Categories: Amazon, AWS, utility ============================================================================== bamtools ============================================================================== Description: C++ API & command-line toolkit for working with BAM data. Versions: 2.5.1; 2.5.2 License: N/A Categories: N/A ============================================================================== basespace ============================================================================== Description: BaseSpace Sequence Hub CLI Versions: 1.5.3 License: N/A Categories: Bioinformatics ============================================================================== bbtools ============================================================================== Description: a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. Versions: 38.96 License: GPLv2 Categories: Bioinformatics ============================================================================== bcftools ============================================================================== Description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF Versions: 1.7; 1.12 License: GPLv2 Categories: Bioinformatics ============================================================================== bcl-convert ============================================================================== Description: Converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. Versions: 4.2.4 License: GPLv2 Categories: Bioinformatics ============================================================================== bcl2fastq2 ============================================================================== Description: The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files. Versions: 2.20.0.422 License: N/A Categories: N/A ============================================================================== beast1 ============================================================================== Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. Versions: 1.10.4 License: N/A Categories: N/A ============================================================================== BEDOPS ============================================================================== Description: BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole- genome analyses across a computational cluster. Versions: 2.4.41 License: GNU GPL v2 Categories: Bioinformatics, Genomics ============================================================================== bedtools2 ============================================================================== Description: Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. Versions: 2.25.0; 2.30.0 License: N/A Categories: N/A ============================================================================== BioGeoBEARS ============================================================================== Description: R package that is designed to perform inference of biogeographic history on phylogenies, and also model testing and model choice of the many different possible models of how biogeography may evolve on a phylogeny(dispersal, vicariance, founder-event speciation, DEC, DIVA, BAYAREA, etc.) Versions: 1.1.1 License: N/A Categories: BioInformatics ============================================================================== bioperl ============================================================================== Description: BioPerl is Perl tools for Bioinformatics, genomics and Life Sciences. Versions: 1.7.2 License: GPLv3 Categories: Bioinformatics ============================================================================== blast-plus ============================================================================== Description: Basic Local Alignment Search Tool. Versions: 2.12.0 License: N/A Categories: N/A ============================================================================== blat ============================================================================== Description: BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm. Versions: 35 License: N/A Categories: N/A ============================================================================== blender ============================================================================== Description: Blender is the free and open source 3D creation suite Versions: 4.0.2 License: GNU General Public License Categories: visualization ============================================================================== Boost ============================================================================== Description: Boost C++ library collection. Versions: 1.78.0 License: http://www.boost.org/users/license.html Categories: Programming, C++, library ============================================================================== bowtie ============================================================================== Description: Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Versions: 1.3.0 License: N/A Categories: N/A ============================================================================== bowtie2 ============================================================================== Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences Versions: 2.4.1; 2.4.2 License: N/A Categories: N/A ============================================================================== breseq ============================================================================== Description: breseq is a computational pipeline for the analysis of short- read re-sequencing data (e.g. Illumina, 454, IonTorrent, etc.). It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome. breseq is intended for microbial genomes (<10 Mb) and re- sequenced samples that are only slightly diverged from the reference sequence (<1 mutation per 1000 bp). Versions: 0.38.1 License: GNU GPL v2 (license) and v3 (copying) Categories: Bioinformatics ============================================================================== Bridger Assembler ============================================================================== Description: Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. Versions: 2014.12.01 License: GNU GENERAL PUBLIC LICENSE Categories: Bioinformatics, Genomics, Healthcare, big data ============================================================================== busco ============================================================================== Description: BUSCO (Benchmarking Universal Single-Copy Orthologs) Versions: 5.5.0 License: GPLv2 Categories: Bioinformatics ============================================================================== bwa ============================================================================== Description: Burrow-Wheeler Aligner for pairwise alignment between DNA sequences. Versions: 0.7.15; 0.7.17 License: N/A Categories: N/A ============================================================================== canu ============================================================================== Description: A single molecule sequence assembler for genomes large and small. Versions: 2.2 License: N/A Categories: N/A ============================================================================== cap3 ============================================================================== Description: CAP3 is DNA Sequence Assembly Program Versions: 2015-02-11 License: N/A Categories: N/A ============================================================================== cd-hit ============================================================================== Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. Versions: 4.7 License: GPLv2 Categories: Bioinformatics ============================================================================== CDO - Climate Data Operators ============================================================================== Description: Command line operators to manipulate and analyse Climate and NWP module Data Versions: 2.0.6 License: N/A Categories: cli, climate ============================================================================== cellpose ============================================================================== Description: cellpose is an anatomical segmentation algorithm written in Python 3. Versions: 2.1.1 License: https://github.com/MouseLand/cellpose/blob/main/LICENSE Categories: Biology, deep-learning, biomedical, cell segmentation, image analysis ============================================================================== cellprofiler ============================================================================== Description: CellProfiler is free, open-source software for quantitative analysis of biological images. Versions: 3.1.9; 4.2.4 License: BSD 3-clause license Categories: Bioinformatics, biology, imaging, analysis ============================================================================== cellranger ============================================================================== Description: Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output Versions: 6.1.2; 7.0.0; 7.0.1; 7.1.0; 7.2.0; 8.0.0 License: GPLv2 Categories: Bioinformatics ============================================================================== cellrangerARC ============================================================================== Description: a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data Versions: 2.0.1; 2.0.2 License: GPLv2 Categories: Bioinformatics ============================================================================== cellrangerATAC ============================================================================== Description: a set of analysis pipelines that process Chromium Single Cell ATAC data Versions: 2.1.0 License: GPLv2 Categories: Bioinformatics ============================================================================== cellrangerDNA ============================================================================== Description: a set of analysis pipelines that process Chromium Single Cell data Versions: 1.1.0 License: GPLv2 Categories: Bioinformatics ============================================================================== centrifuge ============================================================================== Description: centrifuge Versions: 1.0.4 License: GNU GPL3 Categories: Bioinformatics ============================================================================== chromHMM ============================================================================== Description: ChromHMM is software for learning and characterizing chromatin states. Versions: 1.24 License: GPLv2 Categories: Bioinformatics ============================================================================== Circos ============================================================================== Description: Circos is a software package for visualizing data and information. Versions: 0.69-8 License: GNU GPL v3 Categories: Bioinformatics, Visualization, Circular ============================================================================== clang ============================================================================== Description: A front-end and tooling infrastructure for languages in the C language family Versions: 14.0.6; 2022.1.2 License: Apache License Categories: compilier c ============================================================================== clustal-omega ============================================================================== Description: Clustal Omega: the last alignment program you'll ever need. Versions: 1.2.4 License: N/A Categories: N/A ============================================================================== CMake ============================================================================== Description: CMake cross-platform make system. Versions: 3.22.2; 3.26.3 License: https://cmake.org/licensing/ Categories: Utility, programming, compiler ============================================================================== code-server ============================================================================== Description: Run VS Code on any machine anywhere and access it in the browser. Versions: 4.8.3 License: MIT Categories: file management, software development, scripting, IDE. ============================================================================== COMSOL ============================================================================== Description: COMSOL is multiphysics simulation software. Versions: 6.0; 6.1 License: https:/www.comsol.com/documentation/6.0/COMSOL_SoftwareLicense Agreement.pdf Categories: Multiphysics, simulation ============================================================================== CONVERGE ============================================================================== Description: [SPECIAL LICENSE REQUIRED: You must provide your own license to use this software] CONVERGE is a CFD code with adaptive meshing. Versions: 3.1.8 License: Provided by licensed labs Categories: Fluid dynamics, CFD, adaptive mesh ============================================================================== Coq ============================================================================== Description: Coq is a formal proof management system. Versions: 8.4pl5 License: GNU Lesser General Public License (LGPL) version 2.1 Categories: proof, Gallina ============================================================================== CPLEX ============================================================================== Description: CPLEX is a high-performance optimizer for linear programming Versions: 12.6.2; 12.9; 20.1.0 License: https://developer.ibm.com/academic/ Categories: optimizer, linear programming ============================================================================== CUBIT ============================================================================== Description: CUBIT is a full-featured software toolkit for robust generation of two- and three-dimensional finite element meshes. Versions: 13.2 License: https://cubit.sandia.gov/public/licensing.html Categories: mesh ============================================================================== cuda ============================================================================== Description: CUDA compilers and libraries. Versions: 10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0; 12.1.1; 12.3.0 License: http://docs.nvidia.com/cuda/eula/index.html Categories: CUDA, gpu, library, programming ============================================================================== cudnn ============================================================================== Description: cuDNN libraries. Versions: 10.2-v8.3.1; 11.2-v8.1.1; 11.3-v8.2.1; 11.5-v8.3.1; 11.6-v8.4.1; 11.7-v8.7.0; 11.8-v8.7.0; 12.1-v8.9.0; 12.3-v8.9.6 License: https://docs.nvidia.com/deeplearning/cudnn/sla Categories: CUDA, gpu, library, programming, cuDNN, deep learning, neural network ============================================================================== cufflinks ============================================================================== Description: Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA- Seq samples. Versions: 2.2.1 License: N/A Categories: N/A ============================================================================== CUPTI ============================================================================== Description: CUDA Profiler Tools Interface Versions: 10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0; 12.1.1; 12.3.0 License: http://docs.nvidia.com/cuda/eula Categories: CUDA, gpu, library, programming, Profiler ============================================================================== cutadapt ============================================================================== Description: cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs. Versions: 1.18 License: Public Domain Categories: Bioinformatics, Sequencing ============================================================================== dalton ============================================================================== Description: A powerful tool for a wide range of molecular properties at different levels of theory Versions: 2020.1-3000mo400mc; 2020.1-gcc; 2020.1-intel-mpi; 2020.1-intel License: N/A Categories: Electronic Structure, Ab Initio, Density Functional Theory ============================================================================== DeepLabCut ============================================================================== Description: DeepLabCut™ is an efficient method for 2D and 3D markerless pose estimation Versions: 2.1.10.4; 2.2.3; 2.3.9 License: GPLv3 Categories: Bioinformatics ============================================================================== Delft3DFM ============================================================================== Description: Delft3DFM is a hydrodynamic numerical model for simulating fluid flow and sediment transport in rivers, estuaries, and coastal regions. Versions: 142431; 2021.03 License: https://oss.deltares.nl/web/delft3dfm/source-code-license Categories: hydrodynamic modeling, sediment transport modeling, river modeling, coastal modeling ============================================================================== delly2 ============================================================================== Description: Delly2 is an integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single- nucleotide resolution in short-read massively parallel sequencing data.. Versions: 0.9.1 License: N/A Categories: N/A ============================================================================== DIAMOND ============================================================================== Description: Accelerated BLAST compatible local sequence aligner Versions: 2.1.8.162 License: GPL-3.0 License Categories: Bioinformatics ============================================================================== dorado ============================================================================== Description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Versions: 0.3.0; 0.3.1; 0.3.4; 0.4.1; 0.4.3; 0.5.3 License: GPLv2 Categories: Bioinformatics ============================================================================== dorado_server ============================================================================== Description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Versions: 7.3.9 License: GPLv2 Categories: Bioinformatics ============================================================================== dRep ============================================================================== Description: a python program which performs rapid pair-wise comparison of genome sets Versions: 3.4.5 License: GPLv2 Categories: Bioinformatics ============================================================================== Eigen ============================================================================== Description: Linear algebra template library Versions: 3.4.0 License: https://eigen.tuxfamily.org/index.php Categories: Linear algebra, numerical, development, library ============================================================================== elastix ============================================================================== Description: elastix: a toolbox for rigid and nonrigid registration of images. Versions: 5.0.1 License: GPLv2 Categories: Bioinformatics ============================================================================== EnTAP ============================================================================== Description: EnTAP is an eukaryotic non-model annotation pipeline. Versions: 1.0.1 License: GPL-3.0 License Categories: Bioinformatics ============================================================================== epacts ============================================================================== Description: EPACTS - Efficient and Parallelizable Association Container Toolbox Versions: 3.4.2 License: GNU GPL3 Categories: Bioinformatics ============================================================================== Exonerate ============================================================================== Description: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics. Versions: 2.4.0 License: GPLv3 Categories: Bioinformatics, Sequencing, Alignment ============================================================================== fastANI ============================================================================== Description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI) Versions: 1.34 License: GPLv2 Categories: Bioinformatics ============================================================================== fastcn ============================================================================== Description: A pipeline for the fast estimation of copy-number based on read depth using the multi-mapper mrsFAST. Versions: 1.0 License: GPL Categories: Bioinformatics ============================================================================== fastqc ============================================================================== Description: A quality control tool for high throughput sequence data. Versions: 0.11.5; 0.11.9; 0.12.1 License: N/A Categories: N/A ============================================================================== fasttree ============================================================================== Description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Versions: 2.1.10 License: GPLv3 Categories: Bioinformatics ============================================================================== fastx-toolkit ============================================================================== Description: A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing Versions: 0.0.14 License: GNU Affero General Public License Categories: Bioinformatics, sequencing ============================================================================== fdmnes ============================================================================== Description: FDMNES is an ab initio, free and open source, parallelled under MPI, code which calculates the XANES, RXS and XMCD spectra. Versions: 2016.07.15; 2019.07.19; 2021.05.03; 2022.06.15 License: free and open source Categories: Geometric and electronic structure, near-edge, ab initio ============================================================================== FDTD Solutions ============================================================================== Description: Lumerical FDTD Solutions is a high performance 3D FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials. Versions: 2022R1.4 License: Academic Research Categories: FDTD, maxwell, design, solver, analysis, optimization, optics, photonics, 3D ============================================================================== FEKO ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu] Feko is a computational electromagnetics software. Versions: 2021.2; 2022.1 License: https://caen.engin.umich.edu/software/licensing/ Categories: computational electromagnetics ============================================================================== FFMPEG ============================================================================== Description: FFMPEG is a complete, cross-platform solution to record, convert and stream audio and video. Versions: 4.4.2; 5.1.2; 6.0.0 License: https://ffmpeg.org/legal.html Categories: audio, video, codec, transcoder ============================================================================== fftw ============================================================================== Description: Libraries for computation of discrete Fourier transform. Versions: 3.3.10 License: http://www.fftw.org/fftw3_doc/License-and-Copyright.html Categories: Library, Development, Core ============================================================================== figtree ============================================================================== Description: FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST. Versions: 1.4.4 License: N/A Categories: N/A ============================================================================== fiji ============================================================================== Description: fiji is just ImageJ Versions: 1.5.3 License: GPLv2 Categories: Bioinformatics ============================================================================== FreeSurfer ============================================================================== Description: FreeSurfer MRI processing and analysis software. Versions: 6.0.0; 7.2.0; 7.4.1 License: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLi cense Categories: MRI, neuroimaging, neuroscience ============================================================================== FSL ============================================================================== Description: FSL suite of MRI neuroimaging tools. Versions: 6.0.1; 6.0.5.2 License: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence Categories: fMRI, DTI, neuroimaging, neuroscience ============================================================================== funannotate ============================================================================== Description: Funannotate is a genome prediction, annotation, and comparison software package. Versions: 1.8.4 License: ??? Categories: Bioinformatics gene genefinding genetics ============================================================================== gatk ============================================================================== Description: Toolkit for variant discovery and genotyping Versions: 3.7; 4.3.0.0; 4.2.2.0 License: Broad Institute Software License Agreement Categories: Bioinformatics ============================================================================== Gaussian ============================================================================== Description: Gaussian is an electronic structure program. Versions: 09-revD01; 16-revA03-avx2; 16-revC01-avx2 License: Academic, noncommercial research and instructional use only. Categories: electronic structure, molecular ============================================================================== gcc ============================================================================== Description: GNU compiler suite Versions: 10.3.0; 11.2.0; 13.2.0; 8.2.0 License: GPL Categories: Compiler, programming, development ============================================================================== GDAL ============================================================================== Description: GDAL is a translator library for raster and vector geospatial data formats. Versions: 3.5.1; 3.8.3 License: https://gdal.org/license.html Categories: GIS, geospatial, raster, vector, graphics ============================================================================== GDC Data Transfer Tool ============================================================================== Description: The GDC Data Transfer Tool is a utility for transferring data to and from the Genomic Data Commons (GDC), facilitating the efficient exchange of genomic and clinical data. Versions: 1.6.1 License: N/A Categories: genomic data, data transfer, bioinformatics ============================================================================== GEOS ============================================================================== Description: OpenGIS Simple Features for SQL spatial predicate functions and spatial operators. Versions: 3.10.2; 3.12.1 License: GNU LGPL v2.1 Categories: GIS, Geometry, OSGeo ============================================================================== git ============================================================================== Description: Git version control software Versions: 2.39.1 License: GPL version 2 Categories: Utility, development, version control ============================================================================== git-annex ============================================================================== Description: Manage large files with git, without storing the file contents in git Versions: 10.20220928 License: AGPL version 3.0 Categories: Utility, development, version control, file management ============================================================================== globus-cli ============================================================================== Description: The CLI provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. Versions: 3.19.0; 3.4.0 License: N/A Categories: Data movement ============================================================================== GLPK ============================================================================== Description: The GNU Linear Programming Kit, GLPK, is a library of ANSI C routines for solving large scale linear programming problems using the revised simplex method. Versions: 5.0 License: https://www.gnu.org/licenses/licenses.html#GPL Categories: Library, Development, Mathematics, Solver ============================================================================== GMT - Generic Mapping Tools ============================================================================== Description: an open source collection of tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x–y plots via contour maps to artificially illuminated surfaces and 3D perspective views. Versions: 5.4.3 License: LGPL Categories: GIS projection map plot geography ============================================================================== Go ============================================================================== Description: The Go programming language is an open source project to make programmers more productive. Versions: 1.18 License: https://go.dev/LICENSE?m=text Categories: Go, Programming, golang ============================================================================== groff ============================================================================== Description: GNU roff Versions: 1.22.4 License: GNU Categories: Bioinformatics ============================================================================== gromacs ============================================================================== Description: GROMACS performs Newtonian simulatons of molecular dynamics. Versions: 2021.7; 2022.2 License: N/A Categories: N/A ============================================================================== GSL ============================================================================== Description: GNU scientific libraries Versions: 2.7; 2.7.1 License: GPL Categories: Programming, library, mathematics ============================================================================== gst-libav ============================================================================== Description: GStreamer plugin for the libav* library. Versions: 1.16.1 License: https://github.com/GStreamer/gst-libav?tab=LGPL-2.1-1-ov- file#readme Categories: multimedia ============================================================================== gubbins ============================================================================== Description: Genealogies Unbiased By recomBinations In Nucleotide Sequences Versions: 2.3.1; 3.3.3 License: GPLv2 Categories: Bioinformatics ============================================================================== guppy ============================================================================== Description: Local accelerated basecalling for Nanopore data Versions: 6.1.2; 6.2.1; 6.3.4; 6.3.8; 6.4.2; 6.4.6; 6.5.7 License: GPLv2 Categories: Bioinformatics ============================================================================== Gurobi ============================================================================== Description: Gurobi optimization problem solver. Versions: 10.0.2; 9.5.1 License: http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf Categories: Optimization, linear programming ============================================================================== Harvest ============================================================================== Description: Harvest is a suite of core-genome alignment and visualization tools Versions: 1.1.2 License: GNU GPL v2 Categories: Bioinformatics, Genomics ============================================================================== HDF5 ============================================================================== Description: HDF5 data libraries and utilities. Versions: 1.10.8; 1.8.22 License: https://www.hdfgroup.org/products/licenses.html Categories: Utility, programming, library ============================================================================== HELIOS ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] HELIOS Generalized Geometry Lattice Analysis package. Includes Casmo and Simulate from teh Studsvik suite. Versions: 1.12 License: N/A Categories: Geometry Lattice Analysis, hexagonal VVER reactors, non-LWR lattices ============================================================================== hisat2 ============================================================================== Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). Versions: 2.2.0 License: N/A Categories: N/A ============================================================================== HMMER ============================================================================== Description: HMMER: biosequence analysis using profile hidden Markov models Versions: 3.1b2 License: GNU GPL v3 Categories: Bioinformatics, Sequencing, Markov ============================================================================== homer ============================================================================== Description: Software for motif discovery and next generation sequencing analysis Versions: 4.11.1 License: N/A Categories: N/A ============================================================================== HPC compilers ============================================================================== Description: Compiler suite. Versions: 22.3 License: https://docs.nvidia.com/hpc-sdk/eula/hpc-sdk-ea-eula.pdf Categories: Compiler, development, debugger, profiler ============================================================================== htslib ============================================================================== Description: C library for high-throughput sequencing data formats. Versions: 1.12; 1.13; 1.9 License: N/A Categories: N/A ============================================================================== humann ============================================================================== Description: HMP Unified Metabolic Analysis Network Versions: 3.6 License: GPLv2 Categories: Bioinformatics ============================================================================== IDL ============================================================================== Description: IDL analysis and visualization software. Versions: 8.5; 8.7.2 License: http://www.harrisgeospatial.com/company/legal/eula.aspx Categories: Visualization ============================================================================== igv ============================================================================== Description: The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. Versions: 2.8.9 License: N/A Categories: N/A ============================================================================== ilastik ============================================================================== Description: Interactive learning and segmentation toolkit. Versions: 1.4.0 License: https://www.ilastik.org/license.html Categories: Machine learning, image classification, image analysis. ============================================================================== Image libraries ============================================================================== Description: Image libraries Versions: 220318 License: more than one Categories: libraries, programming, jpeg, gif, png, jbigkit, tiff, libwebp, lcms2, jasper, ImageMagick ============================================================================== ImageMagick ============================================================================== Description: ImageMagick is used to create, edit, compose, or convert digital images. Versions: 7.1.0-25 License: https://imagemagick.org/script/license.php Categories: libraries, programming, jpeg, gif, png, jbigkit, tiff, libwebp, lcms2 ============================================================================== imagemagick ============================================================================== Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images. Versions: 7.1.0-33 License: N/A Categories: N/A ============================================================================== impi ============================================================================== Description: Intel MPI runtime Versions: 2021.5.1; 2018.4.274 License: GPL Categories: MPI, MPICH, programming ============================================================================== impute2 ============================================================================== Description: IMPUTE2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009. Versions: 2.3.2 License: N/A Categories: N/A ============================================================================== Intel ============================================================================== Description: Intel compiler suite. Versions: 18.0.5; 2022.1.2 License: None provided Categories: Library, Development, Core ============================================================================== Intel VTune Profiler ============================================================================== Description: Intel VTune Profiler is a performance analysis tool for analyzing code execution and identifying performance bottlenecks in applications developed for Intel architectures. Versions: 2022.1.0 License: None Provided Categories: performance analysis, profiling, software optimization ============================================================================== ITK ============================================================================== Description: ITK is an open-source system for medical image processing. Versions: 5.2.1; 5.3.0 License: https://software.intel.com/en-us/license/intel-simplified- software-license Categories: Library, development, image processing, MRI, NIfTI ============================================================================== itk ============================================================================== Description: The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. Versions: 5.2.1 License: N/A Categories: N/A ============================================================================== iVar ============================================================================== Description: iVar is a computational package that contains functions for viral amplicon-based sequencing Versions: 1.2.1 License: GPLv2 Categories: Bioinformatics ============================================================================== JAGS ============================================================================== Description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models. Versions: 4.3.0 License: GNU GPL v2 Categories: Bayesian, Markov, MCMC ============================================================================== JasPer ============================================================================== Description: JasPer is a library for the coding and manipulation of images in the JPEG-2000 format. Versions: 2.0.33 License: https://github.com/jasper- software/jasper/blob/master/LICENSE.txt Categories: JPEG-2000 ============================================================================== jcuda ============================================================================== Description: Java bindings for the CUDA runtime and driver API Versions: 10.1.0 License: GPLv2 Categories: Core ============================================================================== jellyfish ============================================================================== Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Versions: 2.2.8 License: GPLv3 Categories: Bioinformatics ============================================================================== joe ============================================================================== Description: JOE editor. Versions: 4.6 License: https://joe-editor.sourceforge.io/ Categories: Editor, development, utility ============================================================================== Julia ============================================================================== Description: Julia is a high-level, high-performance dynamic language for technical computing. The main homepage for Julia can be found at julialang.org. Versions: 1.7.2; 1.8.2; 1.9.2 License: MIT Licenses Categories: Programming ============================================================================== Kaiju ============================================================================== Description: Fast taxonomic classification of metagenomic sequencing reads using a protein reference database Versions: 1.9.0 License: GPLv3 Categories: Bioinformatics ============================================================================== kallisto ============================================================================== Description: kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. Versions: 0.46.0 License: BSD Simplified 2-Clause Categories: Bioinformatics ============================================================================== Knitro ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu] Knitro is an optimization software library for finding solutions of both continuous optimization models as well as discrete optimization models with integer or binary variables. Knitro is primarily designed for finding local optimal solutions of large scale continuous nonlinear problems. Versions: 10.1.0-z License: https://www.artelys.com/solvers/knitro/ Categories: optimization, nonlinear solver ============================================================================== LAMMPS ============================================================================== Description: LAMMPS is a classical molecular dynamics code that models an ensemble of particles. Versions: 02Aug2023; 23Jun2022; 27May21; 31Mar17; 7Aug19 License: http://lammps.sandia.gov/doc/Section_intro.html#open-source- distribution Categories: molecular dynamics ============================================================================== LAPACK ============================================================================== Description: LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least- squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. Versions: 3.10.1 License: http://www.netlib.org/lapack/LICENSE.txt Categories: Libraries ============================================================================== Launcher ============================================================================== Description: A framework for running large collections of serial or multi- threaded applications Versions: 3.7 License: GPLv2 Categories: Core ============================================================================== LDhat ============================================================================== Description: LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data. Versions: 2.2a License: Unlicensed code Categories: Bioinformatics, Alignment ============================================================================== LDhelmet ============================================================================== Description: LDhelmet is a software program for statistical inference of fine-scale crossover recombination rates from population genetic data. Versions: 1.10 License: GPL-3: https://github.com/popgenmethods/LDhelmet Categories: Bioinformatics, Inference ============================================================================== Leptonica ============================================================================== Description: Image processing and image analysis library Versions: 1.82.0 License: http://www.leptonica.org/about-the-license.html Categories: image processing, image analysis, OCR ============================================================================== LIGGGHTS ============================================================================== Description: LIGGGHTS is an Open Source Discrete Element Method Particle Simulation Software. Versions: 3b38a7d-2020-10-08 License: GPL Categories: molecular dynamics, particulate materials ============================================================================== Linaro Forge ============================================================================== Description: Parallel debugging and profiling tools, DDT and MAP. Versions: 23.0.3 License: Not available Categories: Programming, profiler, debugger, performance ============================================================================== longranger ============================================================================== Description: Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. Versions: 2.2.2 License: GPLv2 Categories: Bioinformatics ============================================================================== LS-DYNA ============================================================================== Description: LS-DYNA finite element analysis software. Versions: R10.2.0; R11.1.0; R12.0.0; R13.1.0; R9.3.1 License: None provided Categories: Finite element, multiphysics, simulation ============================================================================== mafft ============================================================================== Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc. Versions: 7.310 License: http://mafft.cbrc.jp/alignment/software/license66.txt Categories: Bioinformatics, Alignment ============================================================================== magma ============================================================================== Description: Magma is a software package for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. Versions: 2.25-2 License: Restricted; contact ITS Software Services. Categories: Algebra, number theory, algebraic geometry and combinatorics. ============================================================================== makedepf90 ============================================================================== Description: Create Makefile dependency list for Fortran source files. Versions: 2.8.9 License: GNU General Public License v2.0 Categories: development utility, Fortran ============================================================================== mash ============================================================================== Description: Fast genome and metagenome distance estimation using MinHash Versions: 2.3 License: GPLv2 Categories: Bioinformatics ============================================================================== mashtree ============================================================================== Description: Create a tree using Mash distances. Versions: 1.4.6 License: GPLv2 Categories: Bioinformatics ============================================================================== Mathematica ============================================================================== Description: Mathematical and technical computing package. Versions: 12.3.1; 13.2.1 License: http://www.wolfram.com/legal/agreements/wolfram- mathematica.html Categories: Mathematics, symbolic algebra ============================================================================== Matlab ============================================================================== Description: Matlab programming environment. Versions: R2021b; R2022b; R2023b License: N/A Categories: Mathematics, programming, simulation ============================================================================== Matplotlib ============================================================================== Description: Visualization with Python. Versions: 3.5.3 License: https://github.com/matplotlib/matplotlib/tree/main/LICENSE Categories: Programming, python, visualization, graph, image ============================================================================== MCNP ============================================================================== Description: MCNP general-purpose Monte Carlo N-Particle code. Versions: 6.2 License: None provided Categories: simulation, monte carlo, nuclear, radiation transport ============================================================================== medaka ============================================================================== Description: tool to create consensus sequences and variant calls from nanopore sequencing data Versions: 1.7.2 License: GPLv2 Categories: Bioinformatics ============================================================================== megahit ============================================================================== Description: MEGAHIT is an ultra-fast and memory-efficient NGS assemble Versions: 1.2.9 License: GPLv3 Categories: Bioinformatics ============================================================================== melt ============================================================================== Description: Mobile Element Locator Tool (MELT) discovers, annotates, and genotypes non-reference Mobile Element Insertions (MEIs) in Illumina DNA paired-end whole genome sequencing Versions: 2.2.2 License: GPLv2 Categories: Bioinformatics ============================================================================== meme ============================================================================== Description: meme suite: Motif-based sequence analysis tools Versions: 5.5.5 License: GPLv2 Categories: Bioinformatics ============================================================================== metaphlan3 ============================================================================== Description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data Versions: 3.0 License: GPLv2 Categories: Bioinformatics ============================================================================== METIS ============================================================================== Description: METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering Versions: 5.1.0; 5.2.1 License: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download Categories: matrix, matrices, partitioning, ordering ============================================================================== mGEMS ============================================================================== Description: Bacterial sequencing data binning on strain-level based on probabilistic taxonomic classification. Versions: 1.2.0 License: GPLv2 Categories: Bioinformatics ============================================================================== minimap2 ============================================================================== Description: Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Mappy provides a convenient interface to minimap2. Versions: 2.14 License: N/A Categories: N/A ============================================================================== MKL ============================================================================== Description: Intel optimized BLAS/LAPACK libraries, also including FFT and other mathematical and statistical routines. Versions: 2018.0.4 License: https://software.intel.com/en-us/license/intel-simplified- software-license Categories: Library, Development, Core, BLAS, LAPACK ============================================================================== mlst ============================================================================== Description: Scan contig files against traditional PubMLST typing schemes Versions: 2.23.0 License: GNU GPL v3 Categories: Bioinformatics ============================================================================== monocle 3 ============================================================================== Description: A toolkit for analyzing single-cell gene expression experiments Versions: 3.0 License: GPLv2 Categories: Bioinformatics ============================================================================== mothur ============================================================================== Description: The goal of mothur is to have a single resource to analyze molecular data that is used by microbial ecologists. Versions: 1.48.0; 1.46.1 License: GNU GPL v2 Categories: Bioinformatics, Genomics ============================================================================== MPI for Python (mpi4py) ============================================================================== Description: Numerical libraries for use within Python. Versions: 3.1.3 License: https://github.com/mpi4py/mpi4py/blob/master/LICENSE.rst Categories: Programming, python, MPI, mpi4py ============================================================================== MPIFileUtils ============================================================================== Description: Parallel file manipulation utilities. Versions: 0.10.2-arcts License: https://github.com/brockpalen/mpifileutils/blob/master/LICENSE Categories: Utility ============================================================================== MrBayes ============================================================================== Description: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. Versions: 3.2.6; 3.2.7a License: GNU GPL v3 or later Categories: Bioinformatics, phylogenetics, Bayesian, MCMC ============================================================================== MRtrix ============================================================================== Description: MRtrix provides a set of tools to perform various advanced diffusion MRI analyses. Versions: 3.0.3-dfd3360; 3.0.4 License: Mozilla Public License, http://mozilla.org/MPL/2.0/ Categories: fMRI, diffusion-weighted MRI, tractography, neuroimaging ============================================================================== mSWEEP ============================================================================== Description: Fast and accurate bacterial community composition estimation Versions: 1.6.1; 1.6.2 License: GPLv2 Categories: Bioinformatics ============================================================================== mummer ============================================================================== Description: MUMmer Versions: 4.0.0rc1 License: Artistic License 2.0 Categories: Bioinformatics ============================================================================== MUSCLE ============================================================================== Description: MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes - only a handful of command-line options are needed to perform common alignment tasks. Versions: 3.8.31 License: Public Domain (http://www.drive5.com/muscle/manual/license.html) Categories: Bioinformatics, Alignment ============================================================================== N/A ============================================================================== Description: N/A Versions: 2.9.2 License: N/A Categories: N/A ============================================================================== Natural Bond Orbital (NBO) ============================================================================== Description: Computational chemistry program for the analysis of many- electron molecular wavefunctions. Versions: 7.0 License: (c) Copyright 1996-2018 Board of Regents of the University of Wisconsin System on behalf of the Theoretical Chemistry Institute. All rights reserved. Categories: Computational Chemistry, Quantum Chemistry, simulation. ============================================================================== ncftp ============================================================================== Description: NcFTP Client is a set of application programs implementing the File Transfer Protocol. Versions: 3.2.6 License: N/A Categories: N/A ============================================================================== NCO ============================================================================== Description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. Versions: 4.7.2; 5.0.6 License: GNU GPL v1.3 or later Categories: Utilities, netCDF ============================================================================== ncview ============================================================================== Description: Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. It runs on UNIX platforms under X11, R4 or higher. Versions: 2.1.8 License: GNU GPL V3 Categories: netCDF, visual browser, utility ============================================================================== NECAT ============================================================================== Description: NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. Versions: 0.0.1 License: GPLv2 Categories: Bioinformatics ============================================================================== NERS-CLASS-SW ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Software for NERS classses: mcc2-3, rebus, dif3d, twodant. Versions: 1.0 License: N/A Categories: Nuclear ============================================================================== NetCDF ============================================================================== Description: Libraries for creating and manipulating NetCDF files. Versions: 4.6.2; 4.8.1 License: https://www.ucar.edu/terms-of-use Categories: Library, Development, Core ============================================================================== NetCDF Fortran ============================================================================== Description: Libraries for creating and manipulating NetCDF files using Fortran. Versions: 4.5.3 License: https://www.ucar.edu/terms-of-use Categories: Library, Development, Core ============================================================================== NetCDF-CXX ============================================================================== Description: C++ API to the NetCDF-C libraries. Versions: 4.3.1 License: https://www.ucar.edu/terms-of-use Categories: Library, Development, Core ============================================================================== neuron ============================================================================== Description: Simulation environment for building and using computational models of neurons and networks of neurons. Versions: 8.2.0 License: GPLv2 Categories: Bioinformatics ============================================================================== new_fugue ============================================================================== Description: a program that calculates linkage disequilibrium measures from genotype files. Versions: 2010-05-25 License: GPLv2 Categories: Bioinformatics ============================================================================== NumPy ============================================================================== Description: Numerical libraries for use within Python. Versions: 1.22.3 License: https://github.com/numpy/numpy Categories: Programming, numerical library, BLAS, LAPACK, python ============================================================================== OCaml ============================================================================== Description: OCaml is a general-purpose, industrial-strength programming language with an emphasis on expressiveness and safety. Versions: 4.02.0; 4.14.0 License: GNU Lesser General Public License (LGPL) version 2.1 Categories: type safety, programming ============================================================================== OCaml Package Manager ============================================================================== Description: source-based package manager for OCaml. Versions: 2.1.3 License: GNU Lesser General Public License (LGPL) version 2.1 Categories: package manager, programming ============================================================================== octave ============================================================================== Description: GNU Octave is a high-level language, primarily intended for numerical computations. Versions: 7.3.0 License: N/A Categories: N/A ============================================================================== oligoarrayaux ============================================================================== Description: OligoArrayAux is a subset of the UNAFold package for use with OligoArray. Versions: 3.8 License: GPLv2 Categories: Bioinformatics ============================================================================== openblas ============================================================================== Description: BLAS provides standard interfaces for linear algebra, including vector-vector operations, matrix-vector operations, and matrix-matrix operations. Versions: 0.3.19; 0.3.23 License: https://opensource.org/licenses/BSD-3-Clause Categories: Programming, C++, library ============================================================================== OpenFOAM ============================================================================== Description: OpenFOAM is a free, open source CFD software. Versions: v2112; v2212 License: http://www.openfoam.com/documentation/licencing.php Categories: omputational fluid dynamics, CFD, heat transfer ============================================================================== OpenJDK ============================================================================== Description: OpenJDK is a free and open-source implementation of the Java Platform. Versions: 18.0.1.1 License: GPLv2 with linking exception Categories: Java, programming ============================================================================== OpenMPI ============================================================================== Description: OpenMPI implementation of the MPI protocol Versions: 4.1.3; 4.1.4; 4.1.6; 3.1.6 License: https://www.open-mpi.org/community/license.php Categories: Utility, Development, Core ============================================================================== OpenRefine ============================================================================== Description: OpenRefine (previously Google Refine) is a powerful free, open source tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. Versions: 3.7.0 License: BSD 3-Clause New or Revised License (see https://github.com/OpenRefine/OpenRefine/blob/master/LICENSE.t xt) Categories: Data cleaning, big data, data conversion ============================================================================== OpenSim ============================================================================== Description: OpenSim is a powerful and open source tool for modeling and simulation of movement. Versions: 4.4.1 License: http://www.apache.org/licenses/LICENSE-2.0 Categories: musculoskeletal, modeling, simulation ============================================================================== openslide ============================================================================== Description: OpenSlide reads whole slide image files. Versions: 3.4.1 License: N/A Categories: N/A ============================================================================== orca ============================================================================== Description: An ab initio, DFT, and semi-empirical SCF-MO package Versions: 4.2.1; 5.0.3 License: Academic Categories: Chemistry, ab initio ============================================================================== orthofinder ============================================================================== Description: Accurate inference of orthologous gene groups made easy. Versions: 2.3.3 License: GPL Categories: Bioinformatics ============================================================================== Pandas ============================================================================== Description: Data analysis and manipulation. Versions: 1.4.2 License: https://github.com/pandas-dev/pandas Categories: Programming, statistics, data analysis, data management, python ============================================================================== Pandoc ============================================================================== Description: A universal document converter. Versions: 2.17.1.1 License: http://www.gnu.org/copyleft/gpl.html Categories: Utility, document converter, markup ============================================================================== Parabricks ============================================================================== Description: Parabricks is a software suite for performing secondary analysis of next generation sequencing (NGS) of DNA and RNA data Versions: 4.0.1-1 License: Apache License 2.0 https://docs.nvidia.com/clara/parabricks/4. 0.1/documentation/thirdpartysoftwarenotices.html Categories: Genomics, Healthcare, big data, pipelines ============================================================================== Parallel HDF5 (PHDF5) ============================================================================== Description: Parallel HDF5 data libraries and utilities. Versions: 1.12.1 License: https://www.hdfgroup.org/products/licenses.html Categories: Utility, programming, library ============================================================================== Paraview ============================================================================== Description: Paraview data analysis and visualization application. Versions: 5.11.1 License: http://www.paraview.org/license/ Categories: Visualization, data analysis, ============================================================================== perl-modules ============================================================================== Description: Perl addin modules for use with Perl version 5.26.3. Versions: 1.0 License: GPLv2 Categories: Bioinformatics ============================================================================== PGI compilers ============================================================================== Description: Compiler suite. Versions: 20.4 License: http://www.pgroup.com/doc/LICENSE.txt Categories: Compiler, development, debugger, profiler ============================================================================== PGPLOT Graphics Subroutine Library ============================================================================== Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device- independent, and the output can be directed to the appropriate device at run time. Versions: 5.2 License: PGPLOT is not public-domain software. However, it is freely available for non-commercial use. The source code and documentation are copyrighted by California Institute of Technology, and may not be redistributed or placed on public Web servers without permission. The software is provided is'' with no warranty. Categories: Graphics, Plotting Software ============================================================================== picard-tools ============================================================================== Description: A set of tools for working with high-throughput sequencing data Versions: 2.8.1; 3.0.0 License: MIT License, Apache License V2.0 Categories: Bioinformatics ============================================================================== plink ============================================================================== Description: PLINK a whole genome association analysis toolset. Versions: 1.9; 2.0; 2.3a; 2.3a3; 2.3dev; 2.4a4 License: GPLv3 Categories: Bioinformatics ============================================================================== Poetry ============================================================================== Description: Python packaging and dependency management. Versions: 1.6.1 License: https://github.com/python-poetry/poetry Categories: Programming, dependency management, python ============================================================================== Prodigal ============================================================================== Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program. Versions: 2.6.3 License: GPL3 Categories: Bioinformatics gene genefinding genetics ============================================================================== PROJ ============================================================================== Description: PROJ is a generic coordinate transformation software. Versions: 9.0.0; 9.3.1 License: MIT Categories: GIS, Library ============================================================================== prokka ============================================================================== Description: Prokka: rapid prokaryotic genome annotation Versions: 1.14.5 License: GPLv2 Categories: Bioinformatics ============================================================================== py-macs2 ============================================================================== Description: MACS2 Model-based Analysis of ChIP-Seq Versions: 2.2.4 License: N/A Categories: N/A ============================================================================== py-weblogo ============================================================================== Description: WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. Versions: 3.7.12 License: N/A Categories: N/A ============================================================================== PyArrow ============================================================================== Description: In-memory analytics for use within Python. Versions: 8.0.0 License: https://github.com/apache/arrow/blob/master/LICENSE.txt Categories: Programming, python ============================================================================== Pycharm ============================================================================== Description: The Python IDE for Professional Developers Versions: 2022.2.2 License: GPLv3 Categories: Bioinformatics ============================================================================== PyMsBayes ============================================================================== Description: A multi-processing Python wrapper and API for approximate- Bayesian phylgeographical inference Versions: 0.3.7 License: GNU GPL v3 Categories: Python, Bayesian, Phylogeographical, msReject ============================================================================== Python ============================================================================== Description: Python is a general purpose programming language Versions: 3.10.4; 3.11.5; 3.12.1; 3.9.12 License: https://docs.python.org/3/license.html Categories: Programming, language ============================================================================== PyTorch ============================================================================== Description: Python tensor library for deep learning. Versions: 1.12.1; 2.0.1 License: https://pytorch.org/ Categories: Programming, python, machine learning, tensor, GPU ============================================================================== qiime ============================================================================== Description: QIIME. (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. Versions: 1.8.0 License: GPLv2 Categories: Bioinformatics ============================================================================== Quantum ESPRESSO ============================================================================== Description: Quantum ESPRESSO is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale. Versions: 7.1-gpu; 7.1; 7.2 License: http://www2.mmm.ucar.edu/wrf/users/public.html Categories: electronic structure, materials modeling, ab initio quantum chemistry ============================================================================== R ============================================================================== Description: R environment for statistical computing and graphics Versions: 4.2.0; 4.3.1; 4.3.2 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, graphics, big data, data science ============================================================================== r-seurat ============================================================================== Description: Tools for Single Cell Genomics Versions: 4.1.1 License: N/A Categories: N/A ============================================================================== racon ============================================================================== Description: Consensus module for raw de novo DNA assembly of long uncorrected reads. Versions: 1.4.20 License: GPLv2 Categories: Bioinformatics ============================================================================== ragtag ============================================================================== Description: RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Versions: 2.1.0 License: GPLv3 Categories: Bioinformatics ============================================================================== raxml ============================================================================== Description: RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. Versions: 8.2.11; 8.2.12 License: N/A Categories: N/A ============================================================================== Rchipenrich ============================================================================== Description: R libraries necessary for Chipenrich Versions: 3.16 License: GPLv2 Categories: Bioinformatics ============================================================================== rclone ============================================================================== Description: rclone is a command line program to sync files and directories to and from many cloud storage providers Versions: 1.57.0; 1.64.0 License: MIT License Categories: File transfer, Utilities ============================================================================== Rgeospatial ============================================================================== Description: A collection of R geospatial libraries Versions: 2022-08-18; 2023-04-25; 2023-07-01; 2024-01-15 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, graphics, big data, data science, geospatial, geography, spatial, map ============================================================================== Rgiotto ============================================================================== Description: R libraries necessary for Giotto Versions: 1.1.0 License: GPLv2 Categories: Bioinformatics ============================================================================== rmats ============================================================================== Description: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. Versions: 4.0.2 License: N/A Categories: N/A ============================================================================== Rmonocle3 ============================================================================== Description: R libraries necessary for Monocle3 Versions: 1.3.1 License: GPLv2 Categories: Bioinformatics ============================================================================== Rnumbat ============================================================================== Description: An R installation for haplotype-aware CNV calling Versions: 1.2.2 License: GPLv2 Categories: Bioinformatics ============================================================================== Ropenblas ============================================================================== Description: R OpenBLAS provides an optimized library for faster linear algebra computations. Versions: 4.2.0; 4.3.1 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, linear algebra, big data, data science ============================================================================== Rosetta ============================================================================== Description: algorithms for computational modeling and analysis of protein structures Versions: 3.13 License: GPLv2 Categories: Bioinformatics ============================================================================== RSEM ============================================================================== Description: RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. Versions: 1.3.3 License: GPLv2 Categories: Bioinformatics ============================================================================== RSeurat ============================================================================== Description: R libraries necessary for Seurat Versions: 4.3.0; 5.0.1 License: GPLv2 Categories: Bioinformatics ============================================================================== RStudio Server ============================================================================== Description: RStudio Desktop is a graphichal user interface for R. Versions: 2022.07.1; 2022.07.2; 2023.06.1; 2023.09.1 License: AGPL v3 Categories: Statistics, graphics, big data, data science, IDE ============================================================================== Rtidyverse ============================================================================== Description: R Tidyverse environment for statistical computing and graphics Versions: 4.2.0; 4.3.1; 4.3.2 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, graphics, big data, data science, tidyverse ============================================================================== sage ============================================================================== Description: SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab. Versions: 9.6 License: GPL Categories: Mathematics software ============================================================================== saige ============================================================================== Description: SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model Versions: 0.44.6.4; 1.1.6.2 License: BSD Simplified 2-Clause Categories: Bioinformatics ============================================================================== salmon ============================================================================== Description: Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Versions: 1.9.0 License: N/A Categories: N/A ============================================================================== samtools ============================================================================== Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format Versions: 1.13; 1.9 License: N/A Categories: N/A ============================================================================== SAS ============================================================================== Description: SAS statistical system software. Versions: 9.4-TS1M7 License: Not available Categories: Statistics, econometrics ============================================================================== schrodinger ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact drugdiscovery@umich.edu] Schrodinger Suite Versions: 2022-2; 2022-3; 2024-1 License: Paid license for Academic use Categories: chemistry, molecular dynamics ============================================================================== SciPy ============================================================================== Description: Scientific libraries for use within Python. Versions: 1.8.0 License: https://github.com/scipy/scipy Categories: Programming, python, solver ============================================================================== SeisSol ============================================================================== Description: SeisSol is a seismic solver. Versions: 201807_Kaikoura-623-g6f221c5 License: https://github.com/SeisSol/SeisSol/blob/master/LICENSE Categories: Core ============================================================================== seqkit ============================================================================== Description: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang. Versions: 2.3.0 License: N/A Categories: N/A ============================================================================== seqtk ============================================================================== Description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format Versions: 1.3 License: GPLv2 Categories: Bioinformatics ============================================================================== ShellCheck ============================================================================== Description: ShellCheck, a static analysis tool for shell scripts Versions: 0.9.0 License: GPLv3 https://github.com/koalaman/shellcheck/blob/master/LICENSE Categories: Shell, Bash, Linter, static-analysis, developer-tools ============================================================================== shovill ============================================================================== Description: Assemble bacterial isolate genomes from Illumina paired-end reads Versions: 1.1.0 License: GPLv2 Categories: Bioinformatics ============================================================================== Singularity ============================================================================== Description: Program for running containerized applications Versions: 3.10.4; 3.11.1 License: https://github.com/sylabs/singularity/blob/master/LICENSE.md Categories: Container, docker, reproducible research ============================================================================== sklvq ============================================================================== Description: scikit-learning vector quantization Versions: 0.1.2 License: GPLv2 Categories: Bioinformatics ============================================================================== slim ============================================================================== Description: SLiM: An Evolutionary Simulation Framework Versions: 4.0.1 License: GPLv2 Categories: Bioinformatics ============================================================================== SnakeMake ============================================================================== Description: The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Versions: 7.34.2 License: MIT License Categories: python, workflow automation, workflow, management ============================================================================== snippy ============================================================================== Description: Rapid haploid variant calling and core genome alignment Versions: 4.6.0 License: GPLv2 Categories: Bioinformatics ============================================================================== SOAPdenovo-Trans ============================================================================== Description: SOAPdenovo-Trans is a de novo transcriptome assembler designed specifically for RNA-Seq data. Versions: 1.0.5 License: GNU GENERAL PUBLIC LICENSE v3.0 Categories: Bioinformatics, Genomics, Healthcare, big data ============================================================================== sortmerna ============================================================================== Description: a tool for filtering, mapping and OTU-picking NGS reads Versions: 2.1 License: GPLv2 Categories: Bioinformatics ============================================================================== spaceranger ============================================================================== Description: a set of analysis pipelines that process Visium spatial RNA- seq output and brightfield microscope images Versions: 1.3.0; 2.0.0; 2.0.1; 2.1.1; 3.0.0 License: GPLv2 Categories: Bioinformatics ============================================================================== Spack Package Manager ============================================================================== Description: A flexible package manager supporting multiple versions, configurations, platforms, and compilers. Versions: 0.21 License: Apache-2.0 Categories: Software Installation, compiling, package manager ============================================================================== spades ============================================================================== Description: SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. Versions: 3.15.5 License: N/A Categories: N/A ============================================================================== spanki ============================================================================== Description: TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. Versions: 0.0.3 License: N/A Categories: Bioinformatics ============================================================================== spark ============================================================================== Description: Apache Spark is a unified analytics engine for large-scale data processing Versions: 3.2.1 License: Apache, https://www.apache.org/licenses/LICENSE-2.0 Categories: Statistics, big data, data science ============================================================================== sratoolkit ============================================================================== Description: The NCBI SRA Toolkit enables reading ('dumping') of sequencing files from the SRA database and writing ('loading') files into the .sra format. Versions: 2.10.9 License: N/A Categories: N/A ============================================================================== Stacks ============================================================================== Description: Stacks is a software pipeline for building loci from short- read sequences, such as those generated on the Illumina platform Versions: 2.65 License: N/A Categories: Bioinformatics, Assembly ============================================================================== star ============================================================================== Description: STAR is an ultrafast universal RNA-seq aligner. Versions: 2.7.11a; 2.7.6a License: N/A Categories: N/A ============================================================================== Star-CCM+ ============================================================================== Description: Star-CCM+ is a CFD application that supports parallel processing. Versions: 17.04.007-R8; 17.04.007 License: Academic Research Categories: CFD ============================================================================== Stata/MP ============================================================================== Description: Statistical analysis software. Versions: 17; 18 License: http://www.stata.com/order/end-user-license-agreement/ Categories: Statistics, econometrics ============================================================================== Stata/SE ============================================================================== Description: Statistical analysis software. Versions: 17; 18 License: http://www.stata.com/order/end-user-license-agreement/ Categories: Statistics, econometrics ============================================================================== stringtie ============================================================================== Description: Transcript assembly and quantification for RNA-Seq Versions: 2.2.1; 2.1.7 License: GPLv2 Categories: Bioinformatics ============================================================================== Subread ============================================================================== Description: Subread package: high-performance read alignment, quantification and mutation discovery Versions: 2.0.3 License: GPLv3 Categories: Bioinformatics ============================================================================== swig ============================================================================== Description: SWIG is an interface compiler. Versions: 3.0.12 License: http://www.swig.org/legal.html Categories: Programming, compiler ============================================================================== szip ============================================================================== Description: Szip is a compression library used with HDF5. Versions: 2.1.1 License: https://www.hdfgroup.org/doc_resource/SZIP/ Categories: Utility, compression ============================================================================== tabix ============================================================================== Description: A useful tool that indexes large .vcf files Versions: 1.7-2 License: GPLv2 Categories: Bioinformatics ============================================================================== table2asn ============================================================================== Description: table2asn is a command-line program that creates sequence records for submission to GenBank Versions: 1.26.678 License: GPLv2 Categories: Bioinformatics ============================================================================== TBB ============================================================================== Description: Intel Thread Building Blocks. Versions: 2022.1.2 License: https://software.intel.com/en-us/articles/end-user-license- agreement Categories: Library, development, core, thread ============================================================================== Tecplot 360 & Tecplot Chorus ============================================================================== Description: Plotting and visualization software that gives full control over 2-D and 3-D plot parameters. Versions: 2022r1 License: N/A Categories: plotting, visualization ============================================================================== TensorFlow ============================================================================== Description: Machine learning platform for use within Python. Versions: 2.7.0 License: Apache License 2.0 Categories: Programming, machine learning library, python ============================================================================== TensorRT ============================================================================== Description: An SDK for high-performance deep learning inference. Versions: 11.8-v8.6.1 License: Apache License 2.0 Categories: Programming, Machine Learning, Tensorflow, Inference ============================================================================== terastitcher ============================================================================== Description: A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images Versions: 1.10.18; 1.11.10 License: GPLv3 Categories: Bioinformatics ============================================================================== Tesseract ============================================================================== Description: Optical character recognition, document conversion, text processing Versions: 5.2.0 License: https://github.com/tesseract-ocr/tesseract/blob/main/LICENSE Categories: image processing, image analysis, OCR, optical character recognition, document conversion, text processing ============================================================================== themisto ============================================================================== Description: Themisto is a succinct colored de Bruijn graph supporting pseudo-alignment Versions: 1.0; 2.1.0 License: GPLv2 Categories: Bioinformatics ============================================================================== tmux ============================================================================== Description: Terminal multiplexer Versions: 3.3a License: https://opensource.org/licenses/ISC Categories: Terminal, multiplex ============================================================================== tophat ============================================================================== Description: TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. Versions: 2.1.1 License: GPLv3 Categories: Bioinformatics ============================================================================== TractSeg ============================================================================== Description: Tool for fast and accurate white matter bundle segmentation from Diffusion MRI. Versions: 2.8 License: GPLv2 Categories: Bioinformatics ============================================================================== trimgalore ============================================================================== Description: Trim Galore! is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. Versions: 0.6.7 License: N/A Categories: N/A ============================================================================== trimmomatic ============================================================================== Description: Trimmomatic: A flexible read trimming tool for Illumina NGS data Versions: 0.36 License: GNU GPL v3 Categories: Bioinformatics, Sequencing ============================================================================== Trinity ============================================================================== Description: Trinity assembles transcript sequences from Illumina RNA-Seq data. Versions: 2.12.0; 2.15.1 License: https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/ master/LICENSE Categories: Bioinformatics, Assembly, Transcriptome ============================================================================== UCSC-utilities ============================================================================== Description: UCSC Genome Browser Utilites. Versions: 4.0.0 License: http://genome.ucsc.edu/license/ Categories: Bioinformatics ============================================================================== UCX ============================================================================== Description: Unified Communication X (UCX) Versions: 1.14.1 License: https://github.com/openucx/ucx?tab=License-1-ov-file#readme Categories: Communication ============================================================================== unrar ============================================================================== Description: unrar is a utility from RARLAB for extracting RAR archives. Versions: 6.12 License: UnRAR is freeware. See $UNRAR_HOME/license.txt Categories: utility, archive ============================================================================== use.own ============================================================================== Description: Module to add personal module directory to module path. Versions: False License: None Categories: utility ============================================================================== valgrind ============================================================================== Description: An instrumentation framework for building dynamic analysis. Versions: 3.20.0 License: N/A Categories: N/A ============================================================================== VASP ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu] VASP, The Vienna Ab initio simulation package, a plane wave electronic structure code. Versions: 5.4.4.18Apr17.p1; 5.4.4.18Apr17.p1.sol; 6.4.2; 6.4.2.sol License: https://www.vasp.at/index.php/faqs Categories: electronic structure code, molecular dynamics ============================================================================== vcflib ============================================================================== Description: vcflib is both a C++ library and cmdline tools for parsing and manipulating VCF files. Versions: 1.0.1+dfsg-3 License: MIT Categories: bioinformatics, genomics, VCF ============================================================================== vcftools ============================================================================== Description: VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. Versions: 0.1.15 License: GPLv3 Categories: N/A ============================================================================== verkko ============================================================================== Description: Verkko is implemented as a Snakemake workflow, launched by a wrapper script to parse options and create a config.yml file. Versions: 1.4.1 License: GPLv2 Categories: Bioinformatics ============================================================================== VESTA ============================================================================== Description: VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Versions: 3.5.8 License: https://jp-minerals.org/vesta/en/doc/VESTAli1.html Categories: Chemistry ============================================================================== VisIt ============================================================================== Description: VisIt data analysis and visualization application. Versions: 3.3.1 License: N/A Categories: Visualization, data analysis ============================================================================== VLC ============================================================================== Description: VLC media player Versions: 3.0.9 License: GPLv2 Categories: Bioinformatics ============================================================================== Wannier90 ============================================================================== Description: Maximally-localised Wannier functions (MLWFs) and Wannier90 Versions: 1.2 License: http://www.wannier.org Categories: MLWFs, electronic structure code ============================================================================== whisper ============================================================================== Description: Whisper is a general-purpose speech recognition model. Versions: v20230314 License: MIT License https://github.com/openai/whisper/blob/main/LICENSE Categories: Bioinformatics, Sequencing ============================================================================== WIEN2k ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu] WIEN2k allows performing electronic structure calculations of solids using density functional theory (DFT), based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method Versions: 23.2-mpi; 23.2-omp; 23.2 License: http://www.wien2k.at/order/index.html Categories: Licenced ============================================================================== wigToBigWig ============================================================================== Description: Convert ascii format wig file to binary big wig format Versions: 4.0.0 License: GPLv2 Categories: Bioinformatics ============================================================================== Wine32 ============================================================================== Description: Wine is a compatibility layer that allows Windows applications to run on Linux and macOS. Versions: 3.0.3 License: https://www.winehq.org/about Categories: compatibility layer ============================================================================== winnowmap ============================================================================== Description: Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads Versions: 2.03 License: GNU GPL v3 Categories: Bioinformatics ============================================================================== XCrySDen ============================================================================== Description: XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. Versions: 1.6 License: GPLv2 Categories: Chemistry ============================================================================== Yasm ============================================================================== Description: Yasm assembler. Versions: 1.3.0; 2.15.05 License: https://github.com/yasm/yasm/blob/master/BSD.txt Categories: assembler, programming ==============================================================================