---------------------------------------------------------------------------- The following is a list of the modules and extensions currently available: ---------------------------------------------------------------------------- ABAQUS: ABAQUS/2022-hotfix-2223, ABAQUS/2023-hotfix-2341 Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. ABRA2: ABRA2/2.23 Assembly Based ReAligner ABRicate: ABRicate/1.0.0 Mass screening of contigs for antimicrobial and virulence genes ABySS: ABySS/2.2.5 Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler ACTC: ACTC/1.1 ACTC converts independent triangles into triangle strips or fans. ADMIXTURE: ADMIXTURE/1.3.0 ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. AFNI: AFNI/23.1.07, AFNI/24.1.03, AFNI/24.1.11 AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. AMRFinderPlus: AMRFinderPlus/3.12.8 This software and the accompanying database are designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. We have also added "plus" stress, heat, and biocide resistance and virulence factors for some organisms. ANIcalculator: ANIcalculator/1.0 This tool will calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence of tRNA and/or rRNA genes in the fna will artificially inflate the ANI. ANSYS: ANSYS/2023R1, ANSYS/2024R2 ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. ANTLR: ANTLR/2.7.7-Java-11 ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. ANTs: ANTs/2.4.4, ANTs/2.5.0 ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. APR: APR/1.7.0 Apache Portable Runtime (APR) libraries. APR-util: APR-util/1.6.1 Apache Portable Runtime (APR) util libraries. ARAGORN: ARAGORN/1.2.41 a program to detect tRNA genes and tmRNA genes in nucleotide sequences ASTRAL: ASTRAL/5.7.1 ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. ATK: ATK/2.38.0 ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. ATLAS: ATLAS/3.10.2-LAPACK-3.10.1 ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. AUGUSTUS: AUGUSTUS/3.5.0 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Abseil: Abseil/20230125.3 Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives. AmberTools: AmberTools/22.3 AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Anaconda3: Anaconda3/2022.10, Anaconda3/2023.07-2, Anaconda3/2024.02-1 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Apptainer: Apptainer/1.1.8, Apptainer/1.2.3, Apptainer/1.3.3 Apptainer is a portable application stack packaging and runtime utility. It replaces Singularity Archive-Zip: Archive-Zip/1.68 Provide an interface to ZIP archive files. Armadillo: Armadillo/11.4.3-Boost-1.88.0, Armadillo/11.4.3 Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Arrow: Arrow/8.0.0 Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. Aspera-Connect: Aspera-Connect/3.9.6, Aspera-Connect/4.2.6 Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server. AutoDock: AutoDock/4.2.6 AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock-Vina: AutoDock-Vina/1.2.3 AutoDock Vina is an open-source program for doing molecular docking. Autoconf: Autoconf/2.71 Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. Automake: Automake/1.16.4, Automake/1.16.5 Automake: GNU Standards-compliant Makefile generator Autotools: Autotools/20220317 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool BAMM: BAMM/2.5.0 BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. BBMap: BBMap/39.01 BBMap short read aligner, and other bioinformatic tools. BCFtools: BCFtools/1.15.1 Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants BDBag: BDBag/1.6.3 The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles. BEDOPS: BEDOPS/2.4.41 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. BEDTools: BEDTools/2.30.0 BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. BLAST: BLAST/2.14.0-Linux_x86_64 Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. BLAST+: BLAST+/2.13.0 Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. BLAT: BLAT/3.7 BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. BLIS: BLIS/0.9.0 BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. BRAKER: BRAKER/3.0.8 BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes. BUSCO: BUSCO/5.4.5 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs BWA: BWA/0.7.17 Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. BamTools: BamTools/2.5.2 BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. BaseSpaceCLI: BaseSpaceCLI/1.5.3 BaseSpace is a powerful website where biologists and informaticians can easily store, analyze, and share genetic data. BaseSpace is a commerical product from Illumina. BayPass: BayPass/2.41 BayPass is a population genomics software which is primarily designed to identify genetic markers subjected to selection and/or associated with population-specific covariates. BayeScan: BayeScan/2.1 This program, BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model. Bazel: Bazel/5.1.1, Bazel/6.1.0-Python-3.11.3, Bazel/6.1.0, Bazel/6.3.1 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Beagle: Beagle/5.4.27May24.118-Java-21 Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Beast: Beast/1.10.4-CUDA-11.7.0, Beast/2.7.3-CUDA-11.7.0, Beast/2.7.3, ... BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. BeautifulSoup: BeautifulSoup/4.10.0-Python-3.11.3, BeautifulSoup/4.10.0 Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. Bio-DB-HTS: Bio-DB-HTS/3.01 Read files using HTSlib including BAM/CRAM, Tabix and BCF database files Bio-SearchIO-hmmer: Bio-SearchIO-hmmer/1.7.3 Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org. BioPerl: BioPerl/1.7.8 Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Biopython: Biopython/1.76-Python-2.7.18, Biopython/1.79-Python-3.11.3, ... Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. Bismark: Bismark/0.24.0 A tool to map bisulfite converted sequence reads and determine cytosine methylation states Bison: Bison/3.8.2 Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. Blosc: Blosc/1.21.3 Blosc, an extremely fast, multi-threaded, meta-compressor library Boost: Boost/1.79.0, Boost/1.83.0, Boost/1.88.0 Boost provides free peer-reviewed portable C++ source libraries. Boost.MPI: Boost.MPI/1.79.0 Boost provides free peer-reviewed portable C++ source libraries. Boost.Python: Boost.Python/1.79.0 Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. Bottleneck: Bottleneck/1.3.7 Fast NumPy array functions written in C Bowtie: Bowtie/1.3.1 Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. Bowtie2: Bowtie2/2.4.5-Python-2.7.18, Bowtie2/2.4.5 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Bracken: Bracken/2.7 Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. Brotli: Brotli/1.0.9 Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932. Brunsli: Brunsli/0.1 Brunsli is a lossless JPEG repacking library. C3D: C3D/1.4.0 Convert3D Medical Image Processing Tool CAFE5: CAFE5/5.0.0 Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa. CAMB: CAMB/1.5.5 CAMB is a cosmology code for calculating cosmological observables, including CMB, lensing, source count and 21cm angular power spectra, matter power spectra, transfer functions and background evolution. CAT: CAT/5.2.3 CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) CD-HIT: CD-HIT/4.8.1 CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CDBtools: CDBtools/0.99 CDB (Constant DataBase) indexing and retrieval tools for FASTA files CDO: CDO/2.2.0 CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. CFDEMcoupling: CFDEMcoupling/3.8.0 CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple the DEM engine LIGGGHTS to a CFD framework. CFITSIO: CFITSIO/3.49, CFITSIO/4.2.0 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. CGAL: CGAL/4.14.1-Python-2.7.18, CGAL/4.14.3, CGAL/5.6.1 The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. CLHEP: CLHEP/2.4.6.2 The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. CLISP: CLISP/2.49 Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. CMake: CMake/3.11.4, CMake/3.12.1, CMake/3.15.3, CMake/3.23.1, ... CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. CNVnator: CNVnator/0.3.3, CNVnator/0.4.1 a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads COLMAP: COLMAP/3.9-CUDA-11.7.0 COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of features for reconstruction of ordered and unordered image collections. COMSOL: COMSOL/5.6, COMSOL/6.0, COMSOL/6.2, COMSOL/6.3 COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. CONCOCT: CONCOCT/1.1.0-Python-2.7.18 Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. CP2K: CP2K/2023.1 CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. CPLEX: CPLEX/22.1.1 IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability. CPMD: CPMD/4.3 The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. CREST: CREST/2.12 CREST was developed as a utility and driver program for the semiempirical quantum chemistry package xtb. The programs name originated as an abbreviation for Conformer–Rotamer Ensemble Sampling Tool as it was developed as a program for conformational sampling at the extended tight-binding level GFN-xTB. Since then several functionalities have been added to the code. In its current state, the program provides a variety of sampling procedures, for example for improved thermochemistry, or solvation. Generally, CREST functions as an IO-based scheduler for the xtb program and as tool for analyzing structure ensembles. CUDA: CUDA/11.5.2, CUDA/11.7.0, CUDA/11.8.0, CUDA/12.2.0, CUDA/12.4.1, ... CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. CUnit: CUnit/2.1-3 Automated testing framework for C. Caffe: Caffe/1.0-CUDA-11.7.0-Python-3.10.4 Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. CapnProto: CapnProto/0.10.2 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. Cartopy: Cartopy/0.20.3-Python-3.11.3, Cartopy/0.20.3 Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy. Catch2: Catch2/2.13.9 A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later Cbc: Cbc/2.10.5 Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable. CellRanger: CellRanger/7.0.0, CellRanger/8.0.1, CellRanger/9.0.1 Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. CellRanger-ATAC: CellRanger-ATAC/2.1.0 Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. Centrifuge: Centrifuge/1.0.4 Classifier for metagenomic sequences Cereal: Cereal/1.3.0 cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Cgl: Cgl/0.60.8 The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver. CharLS: CharLS/2.4.1 CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios. Check: Check/0.15.2 Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format. CheckM: CheckM/1.0.18-Python-2.7.18, CheckM/1.2.2 CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. CheckM-Database: CheckM-Database/2015_01_16 CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. This is the corresponding database. CheckM2: CheckM2/1.0.1 Rapid assessment of genome bin quality using machine learning. ChemTraYzer: ChemTraYzer/2.1 ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 Chimera: Chimera/1.16-linux_x86_64 UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Circos: Circos/0.69-9 Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. Clang: Clang/12.0.1, Clang/13.0.1 C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. CloudCompare: CloudCompare/2.12.4 3D point cloud and mesh processing software Clp: Clp/1.17.10 Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available. Clustal-Omega: Clustal-Omega/1.2.4 Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms Code_Saturne: Code_Saturne/8.0.1, Code_Saturne/8.3.0 Code_Saturne solves the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows CoinUtils: CoinUtils/2.11.12 CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. Compress-Raw-Zlib: Compress-Raw-Zlib/2.202 Low-Level Interface to zlib or zlib-ng compression library ConnectomeWorkbench: ConnectomeWorkbench/1.5.0 Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. CoordgenLibs: CoordgenLibs/3.0.1 Schrodinger-developed 2D Coordinate Generation CppAD: CppAD/20230000.0 CppAD uses operator overloading of the C++ template class AD to compute derivatives of algorithms defined using AD objects. Cython: Cython/0.27.3, Cython/0.29.33-Python-3.11.3, Cython/0.29.33, ... Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). DB: DB/18.1.40 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. DBD-mysql: DBD-mysql/4.050 Perl binding for MySQL DB_File: DB_File/1.858 Perl5 access to Berkeley DB version 1.x. DBus: DBus/1.14.0 D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. DIAMOND: DIAMOND/2.1.0 Accelerated BLAST compatible local sequence aligner DMTCP: DMTCP/3.0.0 DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. Delft3D: Delft3D/4.04.01-FLOW, Delft3D/2025.01 Simulation of multi-dimensional hydrodynamic flows and transport phenomena, including sediments. Delft3D-FLOW is part of Delft3D 4. DendroPy: DendroPy/4.5.2-Python-2.7.18, DendroPy/4.5.2 A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. DjVuLibre: DjVuLibre/3.5.28 DjVuLibre is an open source (GPL'ed) implementation of DjVu, including viewers, browser plugins, decoders, simple encoders, and utilities. Doxygen: Doxygen/1.9.4 Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. Drishti: Drishti/3.1 Drishti is an open-source scientific visualisation software designed by Ajay Limaye at the National Computational Infrastructure's VizLab. EDirect: EDirect/20.5.20231006 Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats. EIGENSOFT: EIGENSOFT/7.2.1 The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. ELPA: ELPA/2021.11.001, ELPA/2022.05.001 Eigenvalue SoLvers for Petaflop-Applications. EMBOSS: EMBOSS/6.6.0 EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. ESMF: ESMF/8.3.0 The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. EasyBuild: EasyBuild/production, EasyBuild/4.7.1, EasyBuild/4.8.0, ... EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. Eigen: Eigen/3.3.9, Eigen/3.4.0 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Emacs: Emacs/28.1 GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing. EnTAP: EnTAP/1.0.1 EnTAP is an eukaryotic non-model annotation pipeline developed by Alexander Hart and Dr. Jill Wegrzyn of the Plant Computational Genomics Lab at the University of Connecticut with additional support from Dr. Stephen Ficklin and Josh Burns of Washington State University. EnergyPlus: EnergyPlus/23.2.0 EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and water use in buildings. FASTX-Toolkit: FASTX-Toolkit/0.0.14 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. FDMNES: FDMNES/2023_12_22 Finite Difference Method Near Edge Structure is a user friendly ab initio code to simulate X-ray absorption and emission spectroscopies as well as resonant x-ray scattering and x-ray Raman spectroscopies, among other techniques. FDS: FDS/6.7.9, FDS/6.9.1, FDS/6.10.1 Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. FEBio: FEBio/4.5 FEBio is a nonlinear finite element (FE) solver that is specifically designed for biomechanical applications. FFTW: FFTW/3.3.10 FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. FFTW.MPI: FFTW.MPI/3.3.10 FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. FFmpeg: FFmpeg/4.4.2, FFmpeg/5.0.1 A complete, cross-platform solution to record, convert and stream audio and video. FLAC: FLAC/1.3.4 FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality. FLANN: FLANN/1.9.1-Python-3.10.4, FLANN/1.9.1 FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces. FLASH: FLASH/2.2.00 FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. FLTK: FLTK/1.3.8 FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. FPC: FPC/3.2.2 Free Pascal is a mature, versatile, open source Pascal compiler. FSL: FSL/6.0.6.4, FSL/6.0.7.12 FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSLeyes: FSLeyes/1.10.2 FSLeyes is the FSL image viewer. FastANI: FastANI/1.33 FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. FastME: FastME/2.1.6.1 FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. FastQC: FastQC/0.11.9-Java-11, FastQC/0.12.1-Java-11 FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. FastTree: FastTree/2.1.11 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. Fiji: Fiji/2.9.0-Java-8.372 Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1 Fiona: Fiona/1.9.2-Python-3.11.3, Fiona/1.9.2 Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely. Flask: Flask/2.2.2 Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors FlexiBLAS: FlexiBLAS/3.2.0 FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. Flye: Flye/2.9.2 Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. FragGeneScan: FragGeneScan/1.31 FragGeneScan is an application for finding (fragmented) genes in short reads. FreeFEM: FreeFEM/4.12-Python-3.10.4, FreeFEM/4.13-Python-3.10.4, ... FreeFEM offers a fast interpolation algorithm and a language for the manipulation of data on multiple meshes. FreeImage: FreeImage/3.18.0 FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe. FreeSurfer: FreeSurfer/5.3.0-centos6_x86_64, ... FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeXL: FreeXL/1.0.6 FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. FriBidi: FriBidi/1.0.12 The Free Implementation of the Unicode Bidirectional Algorithm. GATE: GATE/9.0-gpu, GATE/9.0 GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography GATK: GATK/3.7-Java-1.8.0_241, GATK/4.3.0.0-Java-11, ... The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. GCC: GCC/11.3.0 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). GCCcore: GCCcore/11.3.0 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). GCTA: GCTA/1.94.1 GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs). GConf: GConf/3.2.6 GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. GD: GD/2.75 GD.pm - Interface to Gd Graphics Library GDAL: GDAL/3.5.0-Python-3.11.3, GDAL/3.5.0, GDAL/3.10.0 GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. GDB: GDB/12.1 The GNU Project Debugger GDRCopy: GDRCopy/2.3, GDRCopy/2.4 A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. GEOS: GEOS/3.10.3 GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) GI-DocGen: GI-DocGen/2023.3 GI-DocGen is a document generator for GObject-based libraries. GObject is the base type system of the GNOME project. GI-Docgen reuses the introspection data generated by GObject-based libraries to generate the API reference of these libraries, as well as other ancillary documentation. GL2PS: GL2PS/1.4.2 GL2PS: an OpenGL to PostScript printing library GLFW: GLFW/3.3.8 GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop GLM: GLM/0.9.9.8 OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. GLPK: GLPK/5.0 The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. GLib: GLib/2.72.1 GLib is one of the base libraries of the GTK+ project GLibmm: GLibmm/2.76.0 C++ bindings for Glib GMAP-GSNAP: GMAP-GSNAP/2023-02-17 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program GMP: GMP/6.2.1 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. GObject-Introspection: GObject-Introspection/1.72.0 GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. GRASP: GRASP/2018 The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms. GRASS: GRASS/8.2.0, GRASS/8.4.0-Python-3.11.3 The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization GROMACS: GROMACS/2023.1-CUDA-11.7.0, GROMACS/2023.1, ... GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI binaries. It also contains the gmxapi extension for the single precision MPI build. GSL: GSL/2.7 The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. GST-plugins-bad: GST-plugins-bad/1.20.2 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. GST-plugins-base: GST-plugins-base/1.20.2 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. GStreamer: GStreamer/1.20.2 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. GTDB-Tk: GTDB-Tk/2.3.2, GTDB-Tk/2.4.0 A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. GTK+: GTK+/3.24.23 GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. GTK2: GTK2/2.24.33 The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. GTK3: GTK3/3.24.33 GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. GTK4: GTK4/4.7.0 GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. GTS: GTS/0.7.6 GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. Garfield++: Garfield++/4.0, Garfield++/5.0-20240801-bugfix, ... Garfield++ is a toolkit for the detailed simulation of particle detectors based on ionisation measurement in gases and semiconductors. Gaussian: Gaussian/g16c01-CUDA-11.7.0 Gaussian provides electronic structure modeling. Gdk-Pixbuf: Gdk-Pixbuf/2.42.8 The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. Geant4: Geant4/10.6-single-thread, Geant4/11.1.2-single-thread, ... Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Geant4-data: Geant4-data/11.1 Datasets for Geant4. GeneMark-ET: GeneMark-ET/4 Eukaryotic gene prediction suite with automatic training GenomeThreader: GenomeThreader/1.7.3-Linux_x86_64-64bit GenomeThreader is a software tool to compute gene structure predictions. GenomeTools: GenomeTools/1.6.2 A comprehensive software library for efficient processing of structured genome annotations. GffCompare: GffCompare/0.12.6 GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. Ghostscript: Ghostscript/9.56.1 Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. GitPython: GitPython/3.1.27 GitPython is a python library used to interact with Git repositories GlobalArrays: GlobalArrays/5.8.1 Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model Globus-CLI: Globus-CLI/3.16.0-Python-3.11.3 A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. GnuCOBOL: GnuCOBOL/3.2 GnuCOBOL (formerly OpenCOBOL) is a free COBOL compiler. cobc translates COBOL source to executable using intermediate C, designated C compiler and linker. GnuTLS: GnuTLS/3.7.8 GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. Go: Go/1.17.6, Go/1.18.3, Go/1.19.13, Go/1.22.1 Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Graphene: Graphene/1.10.8 Graphene is a thin layer of types for graphic libraries GraphicsMagick: GraphicsMagick/1.3.36 GraphicsMagick is the swiss army knife of image processing. Graphviz: Graphviz/2.50.0, Graphviz/5.0.0 Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. GtkSourceView: GtkSourceView/3.24.11 GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor. Guile: Guile/3.0.8 Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. Gurobi: Gurobi/10.0.1-Python-3.10.4 The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. HDF: HDF/4.2.15 HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. HDF5: HDF5/1.10.8, HDF5/1.12.2, HDF5/1.14.0, HDF5/1.14.5 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HEALPix: HEALPix/3.82 Hierarchical Equal Area isoLatitude Pixelation of a sphere. HISAT2: HISAT2/2.2.1 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). HMMER: HMMER/3.3.2 HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. HOOMD-blue: HOOMD-blue/4.0.1-CUDA-11.7.0 HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs. HTSeq: HTSeq/2.0.2 HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. HTSlib: HTSlib/1.15.1, HTSlib/1.17 A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix HarfBuzz: HarfBuzz/4.2.1, HarfBuzz/5.3.1 HarfBuzz is an OpenType text shaping engine. Highway: Highway/1.0.3 Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'. HyPhy: HyPhy/2.5.33 HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning Hypre: Hypre/2.25.0, Hypre/2.33.0 Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. ICA-AROMA: ICA-AROMA/0.4.4-beta ICA-AROMA (i.e. 'ICA-based Automatic Removal Of Motion Artifacts') concerns a data-driven method to identify and remove motion-related independent components from fMRI data. ICU: ICU/71.1, ICU/73.2-Python-3.11.3 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. IDBA-UD: IDBA-UD/1.1.3 IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. IGV: IGV/2.17.1 Integrative Genomics Viewer - desktop genome visualization tool for Mac, Windows, and Linux. IMPUTE2: IMPUTE2/2.3.2_x86_64_dynamic, IMPUTE2/2.3.2_x86_64_static IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 IPython: IPython/8.5.0, IPython/8.14.0-Python-3.11.3 IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. IQ-TREE: IQ-TREE/2.2.2.6, IQ-TREE/2.3.6 Efficient phylogenomic software by maximum likelihood IRFinder-S: IRFinder-S/2.0.1 IRFinder detects intron retention from RNA-Seq experiments. ISA-L: ISA-L/2.30.0 Intelligent Storage Acceleration Library ISL: ISL/0.24 isl is a library for manipulating sets and relations of integer points bounded by linear constraints. ITK: ITK/5.2.1 Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. ITSTool: ITSTool/2.0.7-Python-3.11.3 ITS Tool allows you to translate your XML documents with PO files IgBLAST: IgBLAST/1.21.0-x64-linux IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. ImageMagick: ImageMagick/7.1.0-37 ImageMagick is a software suite to create, edit, compose, or convert bitmap images Imath: Imath/3.1.5 Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics Infernal: Infernal/1.1.4 Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. IntelPython: IntelPython/3.9.16-2023.1.0 Intel® Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel. InterProScan: InterProScan/5.55-88.0, InterProScan/5.66-98.0, ... InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [code only: libraries and external binaries but no data]. JAGS: JAGS/4.3.1, JAGS/4.3.2 JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation Jansson: Jansson/2.14 Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite JasPer: JasPer/2.0.33, JasPer/4.0.0 The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. Java: Java/1.8.0_241, Java/8.372, Java/11.0.18, Java/17.0.6, Java/17.0.9, ... Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Jellyfish: Jellyfish/2.3.0 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. JsonCpp: JsonCpp/1.9.5-Python-3.11.3, JsonCpp/1.9.5 JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. Judy: Judy/1.0.5 A C library that implements a dynamic array. Julia: Julia/1.8.5-linux-x86_64, Julia/1.9.3-linux-x86_64, ... Julia is a high-level, high-performance dynamic programming language for numerical computing JupyterLab: JupyterLab/3.5.0 JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook. KMC: KMC/3.2.1 KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. KaHIP: KaHIP/3.14 The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. Kent_tools: Kent_tools/442 Kent utilities: collection of tools used by the UCSC genome browser. Kraken: Kraken/1.1.1 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Kraken2: Kraken2/2.1.2, Kraken2/2.1.4 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. KronaTools: KronaTools/2.8.1 Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. KyotoCabinet: KyotoCabinet/1.2.80 Kyoto Cabinet is a library of routines for managing a database. LAME: LAME/3.100 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. LAMMPS: LAMMPS/2Aug2023_update2-kokkos-GPU-A100-CUDA-12.2.0, ... LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. LANDIS-II: LANDIS-II/7.0 The LANDIS-II forest landscape model simulates future forests (both trees and shrubs) at decadal to multi-century time scales and spatial scales spanning hundreds to millions of hectares. LAPACK: LAPACK/3.10.1 LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. LASTZ: LASTZ/1.04.03 LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. LCModel: LCModel/6.3 Automatic quantification of in vivo proton MR spectra. LDC: LDC/1.24.0-x86_64, LDC/1.30.0 The LLVM-based D Compiler LERC: LERC/4.0.0 LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds). LIBSVM: LIBSVM/3.30 LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. LLVM: LLVM/14.0.3 The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. LMDB: LMDB/0.9.29 LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. LSD2: LSD2/2.3 Least-squares methods to estimate rates and dates from phylogenies LTR_retriever: LTR_retriever/2.9.0 LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. LZO: LZO/2.10 Portable lossless data compression library Leptonica: Leptonica/1.83.0 Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. LevelDB: LevelDB/1.18 LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. LibLZF: LibLZF/3.6 LibLZF is a very small data compression library. It consists of only two .c and two .h files and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still written in portable C. LibSoup: LibSoup/3.0.8 libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications. LibTIFF: LibTIFF/4.3.0 tiff: Library and tools for reading and writing TIFF data files Libint: Libint/2.7.2-lmax-6-cp2k Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. Lighter: Lighter/1.1.2 Fast and memory-efficient sequencing error corrector LittleCMS: LittleCMS/2.13.1 Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Lua: Lua/5.4.4 Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. M4: M4/1.4.19 GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. MACS2: MACS2/2.2.8 Model Based Analysis for ChIP-Seq data MAFFT: MAFFT/7.505-with-extensions 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. MATIO: MATIO/1.5.23 matio is an C library for reading and writing Matlab MAT files. MATLAB: MATLAB/2023a_Update_1, MATLAB/2023a, MATLAB/2023b_Update_7, ... MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. MCL: MCL/14.137 The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. MCR: MCR/R2016a The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. MDI: MDI/1.4.26-Python-3.11.3, MDI/1.4.26 The MolSSI Driver Interface (MDI) project provides a standardized API for fast, on-the-fly communication between computational chemistry codes. This greatly simplifies the process of implementing methods that require the cooperation of multiple software packages and enables developers to write a single implementation that works across many different codes. The API is sufficiently general to support a wide variety of techniques, including QM/MM, ab initio MD, machine learning, advanced sampling, and path integral MD, while also being straightforwardly extensible. Communication between codes is handled by the MDI Library, which enables tight coupling between codes using either the MPI or TCP/IP methods. MEGA: MEGA/11.0.13 MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles. MEGAHIT: MEGAHIT/1.2.9-Python-2.7.18, MEGAHIT/1.2.9 An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph MEGAN: MEGAN/6.25.10-Java-17 MEGAN is a comprehensive toolbox for interactively analyzing microbiome data MEME: MEME/5.5.3 The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo. META: META/1.7 META is a program for the meta analysis of genome-wide association studies. The program is designed to synthesizing the evidence from different association studies. Particularly, the program is able to work seamlessly with the output of SNPTEST. METIS: METIS/5.1.0 METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. MINC: MINC/2.4.03 Medical Image NetCDF or MINC isn't netCDF. MMseqs2: MMseqs2/14-7e284, MMseqs2/15-6f452 MMseqs2: ultra fast and sensitive search and clustering suite MOSEK: MOSEK/9.3.22 The MOSEK optimization software is designed to solve large-scale mathematical optimization problems. MOSEK main features are listed below. For additional questions, contact our support or browse the online documentation. MPC: MPC/1.2.1 Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal. MPFR: MPFR/4.1.0 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. MPICH: MPICH/4.1.2 MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). MRtrix: MRtrix/3.0.4 MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. MRtrix3Tissue: MRtrix3Tissue/5.2.9-Python-2.7.18 MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software. MUMPS: MUMPS/5.5.1-metis A parallel sparse direct solver MUMmer: MUMmer/4.0.0rc1 MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. MUSCLE: MUSCLE/5.1.0 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. MaSuRCA: MaSuRCA/4.1.0 MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Mako: Mako/1.2.0 A super-fast templating language that borrows the best ideas from the existing templating languages Mamba: Mamba/23.1.0-4 Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. Mambaforge: Mambaforge/23.1.0-4 Mambaforge is based on miniforge and allows you to install the conda package manager with the following features pre-configured: conda-forge set as the default (and only) channel, and support for Mamba in place of Conda. MariaDB: MariaDB/10.9.3 MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. Mash: Mash/2.3 Fast genome and metagenome distance estimation using MinHash Mathematica: Mathematica/13.2.1 Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. Maven: Maven/3.9.3 Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. MaxBin: MaxBin/2.2.7-Python-2.7.18, MaxBin/2.2.7 MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Maxima: Maxima/5.47.0 Maxima is a system for the manipulation of symbolic and numerical expressions. Mercurial: Mercurial/6.2 Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. Meryl: Meryl/1.4 Meryl is a tool for creating and working with DNA sequence k-mers. Mesa: Mesa/22.0.3 Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. MeshLab: MeshLab/2023.12 The open source mesh processing system. Meson: Meson/0.62.1, Meson/0.64.0, Meson/1.1.1-Python-3.11.3, Meson/1.3.2 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. Mesquite: Mesquite/2.3.0 Mesh-Quality Improvement Library MetaBAT: MetaBAT/2.15 MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data MetaEuk: MetaEuk/6 MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metal: Metal/2020-05-05 Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. MicrobeAnnotator: MicrobeAnnotator/2.0.5 Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes. Miniconda2: Miniconda2/4.7.10 Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. Miniconda3: Miniconda3/22.11.1-1, Miniconda3/23.10.0-1 Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. Miniforge3: Miniforge3/24.7.1-2 Miniforge is a free minimal installer for conda and Mamba specific to conda-forge. Mono: Mono/6.12.0.122 An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. MosiacHunter: MosiacHunter/1.0.0 A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples. Mothur: Mothur/1.48.1 Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. MrBayes: MrBayes/3.2.7a MrBayes is a program for the Bayesian estimation of phylogeny. MultiQC: MultiQC/1.14 Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Multiwell: Multiwell/2021, Multiwell/2023.1-u Calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems. NAMD: NAMD/2.14-CUDA-11.7.0, NAMD/2.14-CUDA-11.8.0, ... NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NASM: NASM/2.15.05, NASM/2.16.01 NASM: General-purpose x86 assembler NBO: NBO/7.0 The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. NCCL: NCCL/2.12.12-CUDA-11.7.0, NCCL/2.18.3-CUDA-12.2.0, ... The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. NCO: NCO/5.1.3 The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. NGS: NGS/2.11.2 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. NIfTI: NIfTI/2.0.0 Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. NLTK: NLTK/3.7 NLTK is a leading platform for building Python programs to work with human language data. NLopt: NLopt/2.7.1 NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. NSPR: NSPR/4.34 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. NSS: NSS/3.79 Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. NVHPC: NVHPC/22.11-CUDA-11.7.0, NVHPC/23.7-CUDA-12.2.0 C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Nektar++: Nektar++/5.3.0 Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. Nextflow: Nextflow/23.04.2, Nextflow/24.10.2 Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data NiBabel: NiBabel/4.0.2 NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. Nim: Nim/1.6.6 Nim is a systems and applications programming language. Ninja: Ninja/1.10.2, Ninja/1.11.1-Python-3.11.3 Ninja is a small build system with a focus on speed. Nipype: Nipype/1.8.5 Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. ORCA: ORCA/5.0.4, ORCA/6.0.0 ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Octave: Octave/7.1.0 GNU Octave is a high-level interpreted language, primarily intended for numerical computations. OpenBLAS: OpenBLAS/0.3.20 OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. OpenBabel: OpenBabel/3.1.1 Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. OpenCV: OpenCV/4.6.0-contrib OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository. OpenEXR: OpenEXR/3.1.5 OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications OpenFOAM: OpenFOAM/v2206, OpenFOAM/v2212, OpenFOAM/5.0-20180108, ... OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM-Extend: OpenFOAM-Extend/4.1-20210705-Python-2.7.18 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenJPEG: OpenJPEG/2.5.0 OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software. OpenMM: OpenMM/8.0.0-CUDA-12.5.1-Python-3.11.3 OpenMM is a toolkit for molecular simulation. OpenMPI: OpenMPI/3.1.4, OpenMPI/4.1.4-test, OpenMPI/4.1.4 The Open MPI Project is an open source MPI-3 implementation. OpenMolcas: OpenMolcas/22.10 OpenMolcas is a quantum chemistry software package. OpenPGM: OpenPGM/5.2.122 OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. OpenPose: OpenPose/1.7.0 OpenPose is a real-time multi-person system to jointly detect human body, hand, facial, and foot keypoints (in total 135 keypoints) on single images. OpenSSL: OpenSSL/1.1, OpenSSL/3 The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. OpenSlide: OpenSlide/3.4.1-largefiles OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). OpenVDB: OpenVDB/10.0.1 OpenVDB is an Academy Award-winning open-source C++ library comprising a novel hierarchical data structure and a suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production and is now maintained by the Academy Software Foundation (ASWF). OptiX: OptiX/7.6.0 OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms. OrthoFinder: OrthoFinder/2.5.5 OrthoFinder: phylogenetic orthology inference for comparative genomics Osi: Osi/0.108.9 Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming. PAML: PAML/4.10.5 PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PCRE: PCRE/8.45 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE2: PCRE2/10.40 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PDAL: PDAL/2.8.2-Python-3.11.3, PDAL/2.8.2 PDAL is a C++ library for translating and manipulating point cloud data. PETSc: PETSc/3.17.4, PETSc/3.18.3, PETSc/3.19.2, PETSc/3.22.2 PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. PGDSpider: PGDSpider/2.1.1.5 PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). PICI-LIGGGHTS: PICI-LIGGGHTS/3.8.1 UoB Positron Imaging Centre's Improved LIGGGHTS distribution with an emphasis on the Python interface. PICRUSt2: PICRUSt2/2.5.2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Check out the pre-print here. PLINK: PLINK/1.9b_6.21-x86_64, PLINK/2.00a3.6, PLINK/2.00a6.17 Whole-genome association analysis toolset PLUMED: PLUMED/2.8.1-Python-3.11.3, PLUMED/2.8.1 PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. PLY: PLY/3.11-Python-3.11.3, PLY/3.11 PLY is yet another implementation of lex and yacc for Python. PMIx: PMIx/3.2.3, PMIx/4.2.2 Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. POV-Ray: POV-Ray/3.7.0.10 The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. PRANK: PRANK/170427 PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. PROJ: PROJ/9.0.0 Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Pandoc: Pandoc/3.1.2 If you need to convert files from one markup format into another, pandoc is your swiss-army knife Pango: Pango/1.50.7 Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. ParMETIS: ParMETIS/4.0.3 ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. ParMGridGen: ParMGridGen/1.0 ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. ParaView: ParaView/5.4.1-Python-2.7.18-mpi, ... ParaView is a scientific parallel visualizer. Perl: Perl/5.34.1-minimal, Perl/5.34.1, Perl/5.36.1, Perl/5.38.0 Larry Wall's Practical Extraction and Report Language This is a minimal build without any modules. Should only be used for build dependencies. Perl-bundle-CPAN: Perl-bundle-CPAN/5.36.1 A set of common packages from CPAN PhyloBayes-MPI: PhyloBayes-MPI/1.8c A Bayesian software for phylogenetic reconstruction using mixture models Pillow: Pillow/9.1.1-Python-3.11.3, Pillow/9.1.1 Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. Pillow-SIMD: Pillow-SIMD/9.2.0 Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. Pilon: Pilon/1.23-Java-11 Pilon is an automated genome assembly improvement and variant detection tool PnetCDF: PnetCDF/1.12.3 Parallel netCDF: A Parallel I/O Library for NetCDF File Access PolSpice: PolSpice/3.7.5 PolSpice (aka Spice) is a tool to statistically analyze Cosmic Microwave Background (CMB) data, as well as any other diffuse data pixelized on the sphere. Porechop: Porechop/0.2.4-Python-3.10.4 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity PostgreSQL: PostgreSQL/14.4, PostgreSQL/15.2 PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. PuLP: PuLP/2.8.0-Python-3.11.3, PuLP/2.8.0 PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems. PyBioLib: PyBioLib/1.1.988 PyBioLib is a Python package for running BioLib applications from Python scripts and the command line. BioLib is a library of biological data science applications. Applications on BioLib range from small bioinformatics utilities to state-of-the-art machine learning algorithms for predicting characteristics of biological molecules. PyCairo: PyCairo/1.21.0 Python bindings for the cairo library PyCharm: PyCharm/2022.3.2, PyCharm/2024.1.2 PyCharm Community Edition: Python IDE for Professional Developers PyGObject: PyGObject/3.42.1 PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. PyMOL: PyMOL/2.5.0 PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! PyQt-builder: PyQt-builder/1.15.4-Python-3.11.3 PyQt-builder is the PEP 517 compliant build system for PyQt and projects that extend PyQt. It extends the SIP build system and uses Qt’s qmake to perform the actual compilation and installation of extension modules. PyQt5: PyQt5/5.15.5, PyQt5/5.15.10-Python-3.11.3 PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework. PyTorch: PyTorch/1.12.0-CUDA-11.7.0, PyTorch/1.12.0, ... Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. PyVista: PyVista/0.43.8 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK) PyYAML: PyYAML/6.0-Python-3.11.3, PyYAML/6.0 PyYAML is a YAML parser and emitter for the Python programming language. Pysam: Pysam/0.16.0.1-Python-2.7.18, Pysam/0.19.1 Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. Python: Python/2.7.18-bare, Python/2.7.18, Python/3.10.4-bare, ... Python is a programming language that lets you work more quickly and integrate your systems more effectively. Python-Packages: Python-Packages/2.7.18 Extra packages not included in our regular Python 2.7 Python-bundle-PyPI: Python-bundle-PyPI/2023.06-Python-3.11.3 Bundle of Python packages from PyPI QCA: QCA/2.3.5, QCA/2.3.9 Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. QGIS: QGIS/3.40.1 QGIS is a user friendly Open Source Geographic Information System (GIS) QIIME2: QIIME2/2022.11 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QScintilla: QScintilla/2.11.6, QScintilla/2.14.1 QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control QTLtools: QTLtools/1.3.1 QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps. QUAST: QUAST/5.2.0-Python-2.7.18, QUAST/5.2.0, QUAST/5.3.0 QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Qhull: Qhull/2020.2 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Qt5: Qt5/5.13.1, Qt5/5.15.2, Qt5/5.15.5, Qt5/5.15.10 Qt is a comprehensive cross-platform C++ application framework. Qt5Webkit: Qt5Webkit/5.212.0-alpha4-Qt5-5.15.10, Qt5Webkit/5.212.0-alpha4 Qt Port of WebKit. WebKit is an open source web browser engine. Qt6: Qt6/6.5.2 Qt is a comprehensive cross-platform C++ application framework. QtKeychain: QtKeychain/0.13.2, QtKeychain/0.14.3 Platform-independent Qt API for storing passwords securely. QuantumESPRESSO: QuantumESPRESSO/7.1-nompi, QuantumESPRESSO/7.1 Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Qwt: Qwt/6.2.0, Qwt/6.3.0 The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. R: R/4.1.2, R/4.2.1-bare, R/4.2.1, R/4.2.2, R/4.3.2, R/4.4.0, ... R is a free software environment for statistical computing and graphics. R-bundle-Bioconductor: R-bundle-Bioconductor/3.16-R-4.2.2 Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. R-bundle-CRAN: R-bundle-CRAN/2025.05 Bundle of R packages from CRAN RASPA2: RASPA2/2.0.47 RASPA is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials. RAxML: RAxML/8.2.12-hybrid-avx2 RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. RDFlib: RDFlib/4.2.2, RDFlib/5.0.0 RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information. RE2: RE2/2022-06-01, RE2/2023-08-01 RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library. RECON: RECON/1.08 Patched version of RECON to be used with RepeatModeler. RIblast: RIblast/1.2.0 RIblast is ultrafast RNA-RNA interaction prediction software based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis. RMBlast: RMBlast/2.13.0 RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. ROOT: ROOT/6.18.04, ROOT/6.26.10 The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. RSEM: RSEM/1.3.3 RNA-Seq by Expectation-Maximization RStudio-Server: RStudio-Server/2022.07.2+576-Java-11-R-4.1.2, ... This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: rserver ... --database-config-file="${MYTMP}/db.conf" Racon: Racon/1.5.0 Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. RapidJSON: RapidJSON/1.1.0 A fast JSON parser/generator for C++ with both SAX/DOM style API Rcorrector: Rcorrector/1.0.6 Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. RegTools: RegTools/1.0.0 RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. Relion: Relion/5.0-withPython, Relion/5.0 RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). RepeatMasker: RepeatMasker/4.1.5 RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. RepeatModeler: RepeatModeler/2.0.4 RepeatModeler is a de novo transposable element (TE) family identification and modeling package. RepeatScout: RepeatScout/1.0.6 De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 ) Rmath: Rmath/4.0.4 Rmath is the standalone version of the R math library. Rmath can be used in your own C/C++ routines. Roary: Roary/3.13.0 Rapid large-scale prokaryote pan genome analysis Ruby: Ruby/3.0.5 Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. Rust: Rust/1.60.0, Rust/1.65.0, Rust/1.70.0-Python-3.11.3, Rust/1.78.0, ... Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. SAMtools: SAMtools/1.3.1, SAMtools/1.13, SAMtools/1.16.1, SAMtools/1.21 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. SCOTCH: SCOTCH/7.0.1 Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. SCons: SCons/4.4.0 SCons is a software construction tool. SDL2: SDL2/2.0.22 SDL: Simple DirectMedia Layer, a cross-platform multimedia library SDSL: SDSL/2.1.1-20191211 The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. SEPP: SEPP/4.5.1 SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. SHAPEIT: SHAPEIT/2.r904.glibcv2.17 SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. SIP: SIP/6.8.1-Python-3.11.3 SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. SKESA: SKESA/2.4.0_saute.1.3.0_1 SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs. SLEPc: SLEPc/3.17.2, SLEPc/3.18.3, SLEPc/3.22.2 SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. SLiM: SLiM/4.0.1, SLiM/4.3, SLiM/5.0 SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. SOCI: SOCI/4.0.3-Boost-1.83.0, SOCI/4.0.3-Boost-1.88.0, SOCI/4.0.3 SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. SPAdes: SPAdes/3.15.5-Python-2.7.18, SPAdes/3.15.5, SPAdes/4.0.0 Genome assembler for single-cell and isolates data sets SQLite: SQLite/3.38.3, SQLite/3.42.0 SQLite: SQL Database Engine in a C Library SRA-Toolkit: SRA-Toolkit/3.0.3, SRA-Toolkit/3.0.5 The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format SRPRISM: SRPRISM/3.0.0 Single Read Paired Read Indel Substitution Minimizer SSPACE_Basic: SSPACE_Basic/2.1.1 Scaffolding Pre-Assemblies After Contig Extension (SSPACE) SSW: SSW/1.1 SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. STAR: STAR/2.7.10b STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. SUMO: SUMO/1.19.0 SUMO (Simulation of Urban MObility) is an open source, highly portable, microscopic and continuous multi-modal traffic simulation package designed to handle large networks. SUNDIALS: SUNDIALS/6.3.0 SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers SUPPA: SUPPA/2.3 A tool to study splicing across multiple conditions at high speed and accuracy. SWIG: SWIG/4.0.2 SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Salmon: Salmon/1.5.2, Salmon/1.9.0, Salmon/1.10.1 Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Sambamba: Sambamba/1.0.1 Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. ScaFaCoS: ScaFaCoS/1.0.1 ScaFaCoS is a library of scalable fast coulomb solvers. ScaLAPACK: ScaLAPACK/2.2.0-fb The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. SciPy-bundle: SciPy-bundle/2020.03-Python-2.7.18, ... Bundle of Python packages for scientific software Scythe: Scythe/0.994 Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. Seaborn: Seaborn/0.9.1-Python-2.7.18, Seaborn/0.12.1-Python-3.11.3, ... Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. SeqAn: SeqAn/2.4.0-Python-2.7.18 SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. SeqKit: SeqKit/2.3.1 SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation SeqLib: SeqLib/1.2.0 C++ interface to HTSlib, BWA-MEM and Fermi. Serf: Serf/1.3.9 The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library Shapely: Shapely/1.8.2-Python-3.11.3, Shapely/1.8.2, Shapely/2.0.1 Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. SoX: SoX/14.4.2 Sound eXchange, the Swiss Army knife of audio manipulation Solids4foam: Solids4foam/2.1 A toolbox for performing solid mechanics and fluid-solid interactions in OpenFOAM. SpaceRanger: SpaceRanger/3.1.3 Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image. SpectrA: SpectrA/1.0.1 Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. Squidpy: Squidpy/1.2.3 Spatial Single Cell Analysis in Python Stata: Stata/16-legacy Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. StringTie: StringTie/2.2.1 StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts Subread: Subread/2.0.4 High performance read alignment, quantification and mutation discovery Subversion: Subversion/1.14.1, Subversion/1.14.2 Subversion is an open source version control system. SuiteSparse: SuiteSparse/5.13.0-METIS-5.1.0 SuiteSparse is a collection of libraries manipulate sparse matrices. SuperLU_DIST: SuperLU_DIST/8.1.0 SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Szip: Szip/2.1.1 Szip compression software, providing lossless compression of scientific data TCLAP: TCLAP/1.2.5 TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary. TRF: TRF/4.09.1 Tandem Repeats Finder: a program to analyze DNA sequences. TRUST4: TRUST4/1.0.7 Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information. TRUST4 supports both single-end and paired-end sequencing data with any read length. TSEBRA: TSEBRA/1.1.2.5 TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER11 and BRAKER22 predicitons to increase their accuracies. TWL-NINJA: TWL-NINJA/0.98-cluster_only Nearly Infinite Neighbor Joining Application. Tcl: Tcl/8.6.12, Tcl/8.6.13 Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. TensorFlow: TensorFlow/2.11.0-CUDA-11.7.0-deeplearn, ... An open-source software library for Machine Intelligence Tk: Tk/8.6.12 Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. Tkinter: Tkinter/2.7.18, Tkinter/3.10.4, Tkinter/3.11.3 Tkinter module, built with the Python buildsystem Tomahawk: Tomahawk/beta-0.7.1 Tomahawk is a machine-optimized library for computing linkage-disequilibrium from population-sized datasets. TopHat: TopHat/2.1.2 TopHat is a fast splice junction mapper for RNA-Seq reads. TractSeg: TractSeg/2.8 Tool for fast and accurate white matter bundle segmentation from Diffusion MRI. It can create bundle segmentations, segmentations of the endregions of bundles and Tract Orientation Maps (TOMs). Moreover, it can do tracking on the TOMs creating bundle-specific tractogram and do Tractometry analysis on those. TransDecoder: TransDecoder/5.5.0 TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Transrate: Transrate/1.0.3 Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. Trim_Galore: Trim_Galore/0.6.10-Python-2.7.18, Trim_Galore/0.6.10 Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). Trimmomatic: Trimmomatic/0.39-Java-11 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. Trinity: Trinity/2.15.1 Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinotate: Trinotate/4.0.1 Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome. UCC: UCC/1.0.0 UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. UCX: UCX/1.13.1, UCX/1.14.1, UCX/1.15.0, UCX/1.16.0 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications UCX-CUDA: UCX-CUDA/1.13.1-CUDA-11.7.0, UCX-CUDA/1.13.1-CUDA-11.8.0, ... Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. UDUNITS: UDUNITS/2.2.28 UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. US-Align: US-Align/20221221 US-align: universal structure alignment of monomeric and complex proteins and nucleic acids UShER: UShER/0.5.0 UShER is now a package consisting of a family of programs for rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes. UnZip: UnZip/6.0 UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality. Unicycler: Unicycler/0.5.0 Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. Unity: Unity/2023.2.18f1 Unity’s real-time 3D development engine lets artists, designers, and developers collaborate to create amazing immersive and interactive experiences. VCFtools: VCFtools/0.1.16 The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. VEP: VEP/107 Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP. VMD: VMD/1.9.4a57 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VSEARCH: VSEARCH/2.22.1 VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. VTK: VTK/8.2.0-Python-2.7.18, VTK/8.2.0, VTK/9.2.2-Python-3.11.3, ... The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. VTune: VTune/2022.3.0 Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Vala: Vala/0.56.14 Vala is a programming language using modern high level abstractions without imposing additional runtime requirements and without using a different ABI compared to applications and libraries written in C. Valgrind: Valgrind/3.20.0 Valgrind: Debugging and profiling tools Vamb: Vamb/3.0.9-CUDA-12.2.0 Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation. VarScan: VarScan/2.4.4-Java-11 Variant calling and somatic mutation/CNV detection for next-generation sequencing data Velvet: Velvet/1.2.10-mt-kmer_191 Sequence assembler for very short reads Vim: Vim/9.0.0950 Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. Voro++: Voro++/0.4.6 Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Wayland: Wayland/1.20.0 Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers. Waylandpp: Waylandpp/1.0.0 Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland. WebKitGTK+: WebKitGTK+/2.40.4 WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit's full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions. WhatsHap: WhatsHap/1.7 WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Wine: Wine/8.17 Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems. X11: X11/20220504 The X Window System (X11) is a windowing system for bitmap displays XBeach: XBeach/20230831 XBeach is a two-dimensional model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and backbarrier during storms. XML-Compile: XML-Compile/1.63 Perl module for compilation based XML processing XML-LibXML: XML-LibXML/2.0207 Perl binding for libxml2 XZ: XZ/5.2.5-test, XZ/5.2.5, XZ/5.4.2 xz: XZ utilities Xerces-C++: Xerces-C++/3.2.4 Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. XlsxWriter: XlsxWriter/3.0.8 A Python module for creating Excel XLSX files Xvfb: Xvfb/1.20.13, Xvfb/21.1.3 Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory. Yasm: Yasm/1.3.0 Yasm: Complete rewrite of the NASM assembler with BSD license Z3: Z3/4.10.2-Python-3.10.4, Z3/4.10.2 Z3 is a theorem prover from Microsoft Research with support for bitvectors, booleans, arrays, floating point numbers, strings, and other data types. This module includes z3_solver, the Python interface of Z3. ZeroMQ: ZeroMQ/4.3.4 ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. Zip: Zip/3.0 Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality Zoltan: Zoltan/3.901 Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit abPOA: abPOA/1.4.1 abPOA is an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation. abriTAMR: abriTAMR/1.0.18 abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. ack: ack/2.14 ack is a tool like grep, optimized for programmers alsa-lib: alsa-lib/1.2.14 The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. angsd: angsd/0.940 Program for analysing NGS data. ant: ant/1.10.11-Java-11, ant/1.10.12-Java-11 Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. any2fasta: any2fasta/0.4.2 Convert various sequence formats to FASTA archspec: archspec/0.1.4 A library for detecting, labeling, and reasoning about microarchitectures argtable: argtable/2.13 Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. arpack-ng: arpack-ng/3.8.0 ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. arrow-R: arrow-R/8.0.0-R-4.2.2 R interface to the Apache Arrow C++ library assimp: assimp/5.2.5 Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data. at-spi2-atk: at-spi2-atk/2.38.0 AT-SPI 2 toolkit bridge at-spi2-core: at-spi2-core/2.48.3 Assistive Technology Service Provider Interface. attrdict3: attrdict3/2.0.2-Python-3.11.3, attrdict3/2.0.2 AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes. awscli: awscli/2.11.21 Universal Command Line Environment for AWS barrnap: barrnap/0.9 Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes. bcl2fastq2: bcl2fastq2/2.20.0 bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. beagle-lib: beagle-lib/3.1.2-CUDA-11.7.0, beagle-lib/4.0.0-CUDA-11.7.0, ... beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. bfactor: bfactor/1.04 bfactor is a program for filtering 3D maps and applying B-factors.. binutils: binutils/2.34, binutils/2.38 binutils: GNU binary utilities bioawk: bioawk/1.0 Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. bmtagger: bmtagger/3.101 Best Match Tagger for removing human reads from metagenomics datasets bokeh: bokeh/2.4.3 Statistical and novel interactive HTML plots for Python bwa-mem2: bwa-mem2/2.2.1 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bzip2: bzip2/1.0.8 bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. c-ares: c-ares/1.18.1 c-ares is a C library for asynchronous DNS requests (including name resolves) cURL: cURL/7.83.0, cURL/8.0.1 libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. cairo: cairo/1.17.4 Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB canu: canu/2.2 Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing cath-tools: cath-tools/0.16.10 Protein structure comparison tools such as SSAP, as used by the Orengo Group in curating CATH. ccache: ccache/4.6.3 Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again cellpose: cellpose/3.1.0-gpu, cellpose/3.1.0 A generalist algorithm for cell and nucleus segmentation (v1.0) that can be optimized for your own data (v2.0) and (NEW) perform image restoration (v3.0). ceres-solver: ceres-solver/2.2.0-CUDA-11.7.0 Ceres Solver 1 is an open source C++ library for modeling and solving large, complicated optimization problems. It can be used to solve Non-linear Least Squares problems with bounds constraints and general unconstrained optimization problems. It is a mature, feature rich, and performant library that has been used in production at Google since 2010. cffi: cffi/1.15.1-Python-3.11.3 C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation. cisTEM: cisTEM/2.0.0 cisTEM processes cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. code-server: code-server/4.9.1, code-server/4.19.0 Run VS Code on any machine anywhere and access it in the browser. coverage: coverage/7.2.7 Coverage.py is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not. coverm: coverm/0.6.1-linux-x86_64 CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. cplexAPI: cplexAPI/1.5.1-R-4.4.0 This R Interface to C API of IBM ILOG CPLEX provides CPLEX support for sybil, and requires IBM ILOG CPLEX version >= 12.1 cppy: cppy/1.2.1 A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations. cryptography: cryptography/41.0.1-Python-3.11.3 cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. csvtk: csvtk/0.25.0 A cross-platform, efficient and practical CSV/TSV toolkit in Golang ctffind: ctffind/4.1.14 Program for finding CTFs of electron micrographs. cuDNN: cuDNN/8.4.1.50-CUDA-11.7.0, cuDNN/8.7.0.84-CUDA-11.8.0, ... The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cutadapt: cutadapt/4.2 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. dRep: dRep/3.4.2 dRep is a python program which performs rapid pair-wise comparison of genome sets. One of it’s major purposes is for genome de-replication, but it can do a lot more. dashing: dashing/1.0 Dashing sketches and computes distances between fasta and fastq data. dask: dask/2022.10.0 Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. datamash: datamash/1.8 GNU datamash performs basic numeric, textual and statistical operations on input data files dbus-glib: dbus-glib/0.112 D-Bus is a message bus system, a simple way for applications to talk to one another. dcm2niix: dcm2niix/1.0.20220720, dcm2niix/1.0.20230411 dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. deepTools: deepTools/3.5.2 deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepmedic: deepmedic/0.8.2-CUDA-11.7.0 Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans. desktop-file-utils: desktop-file-utils/0.27 desktop-file-utils contains a few command line utilities for working with desktop entries: * desktop-file-validate: validates a desktop file and prints warnings/errors about desktop entry specification violations. * desktop-file-install: installs a desktop file to the applications directory, optionally munging it a bit in transit. * update-desktop-database: updates the database containing a cache of MIME types handled by desktop files. It requires GLib to compile, because the implementation requires Unicode utilities and such. dill: dill/0.3.6, dill/0.3.7-Python-3.11.3 dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. dorado: dorado/0.3.1-CUDA-11.7.0, dorado/0.5.2-CUDA-11.7.0, ... Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. dotNET-SDK: dotNET-SDK/2.2.203-linux-x64, dotNET-SDK/6.0.101-linux-x64 .NET is a free, cross-platform, open source developer platform for building many different types of applications. double-conversion: double-conversion/3.2.0, double-conversion/3.3.0 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. dropEst: dropEst/0.8.6 Pipeline for initial analysis of droplet-based single-cell RNA-seq data eagle: eagle/1.1.3 Explicit Alternative Genome Likelihood Evaluator ecCodes: ecCodes/2.27.0 ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). edlib: edlib/1.3.9 Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. eggnog-mapper: eggnog-mapper/2.1.9 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. elfutils: elfutils/0.187 The elfutils project provides libraries and tools for ELF files and DWARF data. enchant-2: enchant-2/2.3.3 Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant. epa-ng: epa-ng/0.3.8 EPA-ng - Fast, parallel, highly accurate Maximum Likelihood Phylogenetic Placement, by the team behind RAxML(-ng) espeak-ng: espeak-ng/1.52 The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington. evince: evince/45.0 Evince is a document viewer for multiple document formats. The goal of evince is to replace the multiple document viewers that exist on the GNOME Desktop with a single simple application. exiv2: exiv2/0.27.5 Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. exonerate: exonerate/2.4.0 A continuation of exonerate, a generic tool for sequence alignment by Guy St. C. Slater et al. (formerly at http://www.ebi.ac.uk/~guy/exonerate/). NOTE: do not use the exonerate -c/--cores option, as the multi-threading code contains data races. Multi-threading has been disabled after v2.4.0. expat: expat/2.4.8, expat/2.5.0 Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) expecttest: expecttest/0.1.3 This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output. fast5: fast5/0.6.5 A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data. fastGEAR: fastGEAR/20161216 Inference of recent and ancestral recombination between divergent lineages in bacteria. fastahack: fastahack/1.0.0 Utilities for indexing and sequence extraction from FASTA files. fastp: fastp/0.23.2 A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. fastq-pair: fastq-pair/1.0 Match up paired end fastq files quickly and efficiently. fermi-lite: fermi-lite/20190320 Standalone C library for assembling Illumina short reads in small regions. ffnvcodec: ffnvcodec/11.1.5.2 FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically). file: file/5.43 The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains. filevercmp: filevercmp/20191210 filevercmp function as in sort --version-sort. fixel_combat: fixel_combat/20230526 Performs ComBat data harmonisation on fixel-based data. flatbuffers: flatbuffers/2.0.7, flatbuffers/23.5.26-Python-3.11.3 FlatBuffers: Memory Efficient Serialization Library Includes the Flatbuffers compiler, C/C++ bindings and Python runtime library. flatbuffers-python: flatbuffers-python/2.0, ... Python Flatbuffers runtime library. flex: flex/2.6.4 Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. flit: flit/3.9.0-Python-3.11.3 A simple packaging tool for simple packages. fontconfig: fontconfig/2.14.0 Fontconfig is a library designed to provide system-wide font configuration, customization and application access. foss: foss/2022a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. frealign: frealign/9.11 Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. freebayes: freebayes/1.3.6 Bayesian haplotype-based genetic polymorphism discovery and genotyping. freeglut: freeglut/3.2.2 freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. freetype: freetype/2.10.3, freetype/2.12.1 FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. fsom: fsom/20141119 A tiny C library for managing SOM (Self-Organizing Maps) neural networks. g2clib: g2clib/1.7.0 Library contains GRIB2 encoder/decoder ('C' version). g2lib: g2lib/3.2.0 Library contains GRIB2 encoder/decoder and search/indexing routines. gappa: gappa/0.7.1 gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files. gapseq: gapseq/1.2 gapseq is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. gawk: gawk/5.1.1 The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. gc: gc/8.2.2 The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. gettext: gettext/0.21, gettext/0.21.1 GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation gfbf: gfbf/2022a GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. gffread: gffread/0.12.7 GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. gflags: gflags/2.2.2 The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. giflib: giflib/5.2.1 giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented. git: git/2.36.0-nodocs, git/2.41.0-nodocs Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. git-lfs: git-lfs/3.5.1 Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com glew: glew/2.1.0, glew/2.2.0-egl The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. glib-networking: glib-networking/2.72.1 Network extensions for GLib glog: glog/0.6.0 A C++ implementation of the Google logging module. gmpy2: gmpy2/2.1.2 GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x gmsh: gmsh/4.11.1 Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. gnuplot: gnuplot/5.4.4 Portable interactive, function plotting utility gofasta: gofasta/0.0.5 Some functions for dealing with alignments, developed to handle SARS-CoV-2 data as part of the COG-UK project. gompi: gompi/2022a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. googletest: googletest/1.11.0, googletest/1.12.1, googletest/1.14.0 Google's framework for writing C++ tests on a variety of platforms gperf: gperf/3.1 GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. graphite2: graphite2/1.3.14 Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world. groff: groff/1.22.4 Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. grpcio: grpcio/1.57.0-Python-3.11.3, grpcio/1.57.0 gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems. gspell: gspell/1.12.2 gspell provides a flexible API to add spell-checking to a GTK application. gubbins: gubbins/2.4.0 Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. gzip: gzip/1.12 gzip (GNU zip) is a popular data compression program as a replacement for compress h5py: h5py/3.7.0, h5py/3.9.0-Python-3.11.3 HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. hatchling: hatchling/1.18.0-Python-3.11.3 Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager. help2man: help2man/1.49.2 help2man produces simple manual pages from the '--help' and '--version' output of other commands. hifiasm: hifiasm/0.19.5 Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. hiredis: hiredis/1.0.2 Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command. hunspell: hunspell/1.7.1 Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding. hwloc: hwloc/1.11.8, hwloc/2.7.1-test, hwloc/2.7.1, hwloc/2.8.0, ... The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. hypothesis: hypothesis/4.57.1-Python-2.7.18, hypothesis/6.46.7, ... Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work. igraph: igraph/0.10.3 igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. imageio: imageio/2.22.2 Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats. imkl: imkl/2022.1.0 Intel oneAPI Math Kernel Library instant-NGP: instant-NGP/18102023-CUDA-11.7.0 Here you will find an implementation of four neural graphics primitives, being neural radiance fields (NeRF), signed distance functions (SDFs), neural images, and neural volumes. In each case, we train and render a MLP with multiresolution hash input encoding using the tiny-cuda-nn framework intel-compilers: intel-compilers/2022.1.0 Intel C, C++ & Fortran compilers (classic and oneAPI) intervaltree: intervaltree/0.1 An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. intervaltree-python: intervaltree-python/3.1.0 A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment. intltool: intltool/0.51.0 intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. iomkl: iomkl/2022a Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). iompi: iompi/2022a Intel C/C++ and Fortran compilers, alongside Open MPI. jbigkit: jbigkit/2.1 JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. jedi: jedi/0.18.1-Python-3.11.3 Jedi - an awesome autocompletion, static analysis and refactoring library for Python. It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. Other features include refactoring, code search and finding references. jemalloc: jemalloc/5.2.1, jemalloc/5.3.0 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. joe: joe/4.6 JOE is a full featured terminal-based screen editor. jq: jq/1.5 jq is a lightweight and flexible command-line JSON processor. json-c: json-c/0.16 JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects. jupyter-contrib-nbextensions: jupyter-contrib-nbextensions/0.7.0 A collection of various notebook extensions for Jupyter jupyter-server: jupyter-server/1.21.0 The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila. k8: k8/1.0 K8 is a JavaScript runtime built on top of Google's v8 JavaScript engine. It provides a resizable binary buffer and synchronous APIs for plain file writing and gzip'd file reading.. kallisto: kallisto/0.48.0 kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. kim-api: kim-api/2.3.0 Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. kineto: kineto/0.4.0 A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters lftp: lftp/4.9.2 LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind. libGLU: libGLU/9.0.2 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. libQGLViewer: libQGLViewer/2.6.4 libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers. libRmath: libRmath/4.2.1 The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications. libSBML: libSBML/5.17.2, libSBML/5.19.7 libSBML (Systems Biology Markup Language library) is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It's not an application itself (though it does come with example programs), but rather a library you embed in your own applications. libXau: libXau/1.0.8 The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. libXdmcp: libXdmcp/1.1.2 The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. libaec: libaec/1.0.6 Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. libaio: libaio/0.3.112 Asynchronous input/output library that uses the kernels native interface. libarchive: libarchive/3.6.1, libarchive/3.6.2 Multi-format archive and compression library libavif: libavif/0.11.1 This library aims to be a friendly, portable C implementation of the AV1 Image File Format, as described here: https://aomediacodec.github.io/av1-avif/ libcerf: libcerf/2.1 libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. libdap: libdap/3.20.11 A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. libdeflate: libdeflate/1.10 Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. libdrm: libdrm/2.4.110 Direct Rendering Manager runtime library. libepoxy: libepoxy/1.5.10 Epoxy is a library for handling OpenGL function pointer management for you libev: libev/4.33 A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs. libevent: libevent/2.1.12 The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. libexif: libexif/0.6.24 A library for parsing, editing, and saving EXIF data. libfabric: libfabric/1.15.1 Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. libffcall: libffcall/2.4 GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters libffi: libffi/3.4.2, libffi/3.4.4 The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. libgcrypt: libgcrypt/1.10.1 Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG libgd: libgd/2.3.3 GD is an open source code library for the dynamic creation of images by programmers. libgdiplus: libgdiplus/6.1 Libgdiplus is the Mono library that provides a GDI+-compatible API on non-Windows operating systems. libgeotiff: libgeotiff/1.7.1 Library for reading and writing coordinate system information from/to GeoTIFF files libgit2: libgit2/1.4.3 libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings. libglvnd: libglvnd/1.4.0 libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. libgpg-error: libgpg-error/1.46 Libgpg-error is a small library that defines common error values for all GnuPG components. libgtextutils: libgtextutils/0.7 ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream libgxps: libgxps/0.3.2 libgxps is a GObject based library for handling and rendering XPS documents. libhandy: libhandy/1.8.2 Building blocks for modern adaptive GNOME apps libharu: libharu/2.3.0 libHaru is a free, cross platform, open source library for generating PDF files. libiconv: libiconv/1.17 Libiconv converts from one character encoding to another through Unicode conversion libidn: libidn/1.41 GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. libidn2: libidn2/2.3.2 Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. libjpeg-turbo: libjpeg-turbo/2.1.3, libjpeg-turbo/2.1.5.1 libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. libmad: libmad/0.15.1b MAD is a high-quality MPEG audio decoder. libnsl: libnsl/2.0.0 The libnsl package contains the public client interface for NIS(YP). libogg: libogg/1.3.5 Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. libopus: libopus/1.3.1 Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec. libpciaccess: libpciaccess/0.16, libpciaccess/0.17 Generic PCI access library. libpng: libpng/1.6.37, libpng/1.6.39 libpng is the official PNG reference library libpsl: libpsl/0.21.1 C library for the Public Suffix List libpthread-stubs: libpthread-stubs/0.5 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. libreadline: libreadline/7.0, libreadline/8.1.2, libreadline/8.2 The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. librsvg: librsvg/2.58.0 Librsvg is a library to render SVG files using cairo. librttopo: librttopo/1.1.0 The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores. libsigc++: libsigc++/3.4.0 The libsigc++ package implements a typesafe callback system for standard C++. libsigsegv: libsigsegv/2.14 GNU libsigsegv is a library for handling page faults in user mode. libsndfile: libsndfile/1.1.0 Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. libsodium: libsodium/1.0.18 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. libspatialindex: libspatialindex/1.9.3 C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API libspatialite: libspatialite/5.0.1 SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. libspectre: libspectre/0.2.12 libspectre is a small library for rendering Postscript documents. It provides a convenient easy to use API for handling and rendering Postscript documents. libtasn1: libtasn1/4.19.0 Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package. libtirpc: libtirpc/1.3.2 Libtirpc is a port of Suns Transport-Independent RPC library to Linux. libtool: libtool/2.4.7 GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. libunistring: libunistring/1.0 This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. libunwind: libunwind/1.6.2 The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications libvips: libvips/8.15.2 libvips is a demand-driven, horizontally threaded image processing library. libvorbis: libvorbis/1.3.7 Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format libvori: libvori/220621 C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package. libwebp: libwebp/1.2.4 WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster. libwpe: libwpe/1.14.1 WPE is the reference WebKit port for embedded and low-consumption computer devices. It has been designed from the ground-up with performance, small footprint, accelerated content rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices. libxc: libxc/5.2.3, libxc/6.2.2 Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. libxcb: libxcb/1.17.0 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. libxml++: libxml++/5.0.3 libxml++ is a C++ wrapper for the libxml XML parser library. libxml2: libxml2/2.9.10, libxml2/2.9.13, libxml2/2.10.3, libxml2/2.11.4 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). libxml2-python: libxml2-python/2.9.13 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). This is the Python binding. libxslt: libxslt/1.1.34 Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). libxsmm: libxsmm/1.17 LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). libyaml: libyaml/0.2.5 LibYAML is a YAML parser and emitter written in C. libzip: libzip/1.9.2 libzip is a C library for reading, creating, and modifying zip archives. lmod: lmod Lmod: An Environment Module System longestrunsubsequence: longestrunsubsequence/1.0.1 Implementation of a solver for the Longest Run Subsequence Problem. Given a sequence as input, compute a longest subsequence such that there is at most one run for every character. lpsolve: lpsolve/5.5.2.11 Mixed Integer Linear Programming (MILP) solver lxml: lxml/4.9.1-Python-3.11.3, lxml/4.9.1 The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. lynx: lynx/2.9.2 lynx is an alphanumeric display oriented World-Wide Web Client lz4: lz4/1.9.3 LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. m6anet: m6anet/2.1.0 m6anet is a python tool that leverages Multiple Instance Learning framework to detect m6a modifications from Nanopore Direct RNA Sequencing data maeparser: maeparser/1.3.0 maeparser is a parser for Schrodinger Maestro files. magma: magma/2.6.2-CUDA-11.7.0, magma/2.7.2-CUDA-12.2.0 The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. make: make/4.3 GNU version of make utility makedepend: makedepend/1.0.7 The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. makeinfo: makeinfo/6.7, makeinfo/6.8 makeinfo is part of the Texinfo project, the official documentation format of the GNU project. manta: manta/1.6.0 Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. matplotlib: matplotlib/2.2.5-Python-2.7.18, ... matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. medaka: medaka/1.9.1-CUDA-11.8.0, medaka/1.9.1 medaka is a tool to create a consensus sequence from nanopore sequencing data. mediaflux-data-mover: mediaflux-data-mover/current mediaflux-data-mover is a data transfer tool for uploading and/or downloading data from a Mediaflux server using a shareable token. mediaflux-explorer: mediaflux-explorer/current mediaflux-explorer is a Java-based GUI application focusing uploads, downloads, queries and sharing of data. metaWRAP: metaWRAP/1.3-Python-2.7.18 MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. minc-stuffs: minc-stuffs/0.1.25 minc-stuffs is repository that houses scripts and bits of code that are useful for performing calculations on and o therwise extracting information from minc files. minc-toolkit: minc-toolkit/1.9.18.2 Medical Image NetCDF or MINC isn't netCDF. minigraph: minigraph/0.20 Minigraph is a sequence-to-graph mapper and graph constructor. minimap2: minimap2/2.24, minimap2/2.26 Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. minizip: minizip/1.1 Mini zip and unzip based on zlib ml_dtypes: ml_dtypes/0.3.2-Python-3.11.3, ml_dtypes/0.3.2 ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including: bfloat16: an alternative to the standard float16 format float8_*: several experimental 8-bit floating point representations including: float8_e4m3b11fnuz float8_e4m3fn float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz mm-common: mm-common/1.0.5 The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries. molmod: molmod/1.4.8 MolMod is a Python library with many compoments that are useful to write molecular modeling programs. morpho-Bundle: morpho-Bundle/0.6.2 Morpho is a programmable environment for shape optimization and scientific computing tasks more generally. morpho-cli: morpho-cli/0.6.2-alpha2 Morpho is a programmable environment for shape optimization and scientific computing tasks more generally. morpho-lib: morpho-lib/0.6.2 Morpho is a programmable environment for shape optimization and scientific computing tasks more generally. morphopm: morphopm/0.1.0-alpha3 Morpho is a programmable environment for shape optimization and scientific computing tasks more generally. morphoview: morphoview/0.6.0-alpha2 Morpho is a programmable environment for shape optimization and scientific computing tasks more generally. motif: motif/2.3.8 Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. mpi4py: mpi4py/3.1.4-Python-3.11.3, mpi4py/3.1.4 MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. multichoose: multichoose/1.0.3 generate multiset combinations (n multichoose k). nanopolish: nanopolish/0.13.3 Software package for signal-level analysis of Oxford Nanopore sequencing data. ncbi-vdb: ncbi-vdb/2.11.2, ncbi-vdb/3.0.2, ncbi-vdb/3.0.5 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. ncdf4: ncdf4/1.17-R-4.2.2 ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files ncdu: ncdu/1.17 Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed. ncurses: ncurses/6.2, ncurses/6.3, ncurses/6.4, ncurses/6.5 The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. ncview: ncview/2.1.8 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. netCDF: netCDF/4.9.0 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netCDF-C++4: netCDF-C++4/4.3.1 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netCDF-Fortran: netCDF-Fortran/4.6.0 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. nettle: nettle/3.8 Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. networkx: networkx/2.8.4 NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. neuroCombat: neuroCombat/0.2.12 ComBat algorithm for harmonizing multi-site imaging data newick_utils: newick_utils/2024-05-06 The Newick Utilities are a suite of programs for working with Newick-formatted phylogenetic trees. nghttp2: nghttp2/1.48.0 This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API. nghttp3: nghttp3/0.6.0 nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation. ngtcp2: ngtcp2/0.7.0 'Call it TCP/2. One More Time.' ngtcp2 project is an effort to implement RFC9000 QUIC protocol. nlohmann_json: nlohmann_json/3.10.5 JSON for Modern C++ nodejs: nodejs/16.15.1, nodejs/18.17.1, nodejs/20.13.1 Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. nose3: nose3/1.3.8 Nose extends unittest to make testing easier. nsync: nsync/1.25.0, nsync/1.26.0-Python-3.11.3 nsync is a C library that exports various synchronization primitives, such as mutexes numactl: numactl/2.0.14, numactl/2.0.16 The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. numba: numba/0.56.4 Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code. numexpr: numexpr/2.8.4 The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. occt: occt/7.5.0p1 Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. ollama: ollama/0.9.1-CUDA-12.5.1 Get up and running with large language models. onedrive: onedrive/2.4.21 A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, OneDrive for Office365 and SharePoint. ont-fast5-api: ont-fast5-api/4.1.1 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. p11-kit: p11-kit/0.24.1 Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process. p7zip: p7zip/17.04 p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. parallel: parallel/20220722 parallel: Build and execute shell commands in parallel parasail: parasail/2.6 parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. parsnp: parsnp/1.5.3 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. patchelf: patchelf/0.15.0, patchelf/0.18.0 PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. pcaudiolib: pcaudiolib/1.3 The Portable C Audio Library (pcaudiolib) provides a C API to different audio devices. picard: picard/2.25.1-Java-11, picard/3.0.0-Java-17 A set of tools (in Java) for working with next generation sequencing data in the BAM format. pigz: pigz/2.7 pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. pixman: pixman/0.40.0 Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. pkg-config: pkg-config/0.29.2 pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). pkgconf: pkgconf/1.8.0, pkgconf/1.9.5 pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. pkgconfig: pkgconfig/1.5.5-python, pkgconfig/1.5.5-Python-3.11.3 pkgconfig is a Python module to interface with the pkg-config command line tool plotly.py: plotly.py/5.12.0 An open-source, interactive graphing library for Python pocl: pocl/1.8 Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard poetry: poetry/1.2.2, poetry/1.5.1-Python-3.11.3 Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere. poppler: poppler/22.12.0 Poppler is a PDF rendering library pplacer: pplacer/1.1.alpha19 Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. prodigal: prodigal/2.6.3 Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. prokka: prokka/1.14.5 Prokka is a software tool for the rapid annotation of prokaryotic genomes. protobuf: protobuf/3.11.4, protobuf/3.19.4, protobuf/24.0 Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data. protobuf-python: protobuf-python/3.11.4, protobuf-python/3.19.4, ... Python Protocol Buffers runtime library. psycopg2: psycopg2/2.9.5-Python-3.11.3, psycopg2/2.9.5 Psycopg is the most popular PostgreSQL adapter for the Python programming language. pugixml: pugixml/1.12.1 pugixml is a light-weight C++ XML processing library pullseq: pullseq/1.0.2 Utility program for extracting sequences from a fasta/fastq file pyBigWig: pyBigWig/0.3.18 A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. pybind11: pybind11/2.9.2, pybind11/2.11.1-Python-3.11.3 pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. pydantic: pydantic/1.10.4 Data validation and settings management using Python type hinting. pydicom: pydicom/2.3.0 Pure python package for DICOM medical file reading and writing. pydot: pydot/1.4.1 Python interface to Graphviz's Dot language. pyfaidx: pyfaidx/0.7.1 pyfaidx: efficient pythonic random access to fasta subsequences pyminc: pyminc/0.57 A python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data. pyproj: pyproj/3.4.0-Python-3.11.3, pyproj/3.4.0 Python interface to PROJ4 library for cartographic transformations pyspoa: pyspoa/0.0.9 Python bindings to spoa. pytest-flakefinder: pytest-flakefinder/1.1.0 Runs tests multiple times to expose flakiness. pytest-rerunfailures: pytest-rerunfailures/11.1 pytest plugin to re-run tests to eliminate flaky failures. pytest-shard: pytest-shard/0.1.2 pytest plugin to support parallelism across multiple machines. Shards tests based on a hash of their test name enabling easy parallelism across machines, suitable for a wide variety of continuous integration services. Tests are split at the finest level of granularity, individual test cases, enabling parallelism even if all of your tests are in a single file (or even single parameterized test method). pytest-xdist: pytest-xdist/2.5.0 xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters. python-igraph: python-igraph/0.10.3 Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis. python-isal: python-isal/1.1.0 Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. python-parasail: python-parasail/1.3.3 Python Bindings for the Parasail C Library qctool: qctool/2.2.0 qctool v2 tool for quality control and analysis of gwas datasets. . qrupdate: qrupdate/1.1.2 qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. re2c: re2c/2.2, re2c/3.1 re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. rgdal: rgdal/1.6-6 Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. ruamel.yaml: ruamel.yaml/0.17.21 ruamel.yaml is a YAML 1.2 loader/dumper package for Python. rush: rush/0.5.0 A cross-platform command-line tool for executing jobs in parallel sagemath: sagemath/10.3, sagemath/10.4 Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab. samclip: samclip/0.4.0 Filter SAM file for soft and hard clipped alignments. scikit-bio: scikit-bio/0.5.7 scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. scikit-build: scikit-build/0.15.0, scikit-build/0.17.6-Python-3.11.3 Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. scikit-image: scikit-image/0.19.3 scikit-image is a collection of algorithms for image processing. scikit-learn: scikit-learn/0.20.4-Python-2.7.18, scikit-learn/1.1.2 Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. screen_assembly: screen_assembly/1.2.7 Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. seqtk: seqtk/1.3 Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. settarg: settarg The settarg module provides a way to connect the loaded modules with your build system by setting environment variables. setuptools: setuptools/63.4.0-Python-3.10.4 Setuptools is a fully-featured, actively-maintained, and stable library designed to facilitate packaging Python projects. setuptools-rust: setuptools-rust/1.6.0-Python-3.10.4, ... setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython. sextractor: sextractor/2.25.0 SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it can perform reasonably well on moderately crowded star fields. shovill: shovill/1.1.0 Faster SPAdes assembly of Illumina reads showq: showq/0.15 sickle: sickle/1.33 Windowed Adaptive Trimming for fastq files using quality silversearcher-ag: silversearcher-ag/2.2.0 A code searching tool similar to ack, with a focus on speed. skani: skani/0.2.2 skani - accurate, fast nucleotide identity calculation for MAGs, genomes, and databases slow5tools: slow5tools/0.4.0 slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. slurm: slurm/latest smithwaterman: smithwaterman/20160702 smith-waterman-gotoh alignment algorithm. snakemake: snakemake/7.22.0, snakemake/8.4.2-Python-3.11.3 The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. snappy: snappy/1.1.9, snappy/1.1.10 Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. snippy: snippy/4.6.0 Rapid haploid variant calling and core genome alignment snp-sites: snp-sites/2.5.1 Finds SNP sites from a multi-FASTA alignment file. snpEff: snpEff/5.0e-Java-11 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). snptest: snptest/2.5.6 SNPTEST is a program for the analysis of single SNP association in genome-wide studies. sonic: sonic/0.2.0 Sonic is a simple algorithm for speeding up or slowing down speech. However, it's optimized for speed ups of over 2X. spaln: spaln/3.0.6b Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. sparsehash: sparsehash/2.0.4 An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. spartan: spartan/rhel9, spartan/2016-03-parallel spoa: spoa/4.0.7 Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences spparks: spparks/20230906 SPPARKS is a parallel Monte Carlo code for on-lattice and off-lattice models that includes algorithms for kinetic Monte Carlo (KMC), rejection kinetic Monte Carlo (rKMC), and Metropolis Monte Carlo (MMC). It implements several KMC solvers whose serial computational complexity ranges from O(N) to O(NlogN) to O(1) in the number of events N owned by a processor. statsmodels: statsmodels/0.13.1 Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. stda: stda/1.6.3.3 stda program for computing excited states and response functions via simplified TD-DFT methods (sTDA, sTD-DFT, and SF-sTD-DFT) sybil: sybil/2.2.0-R-4.4.0 The package sybil is a Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). Sybil has been removed from CRAN due to sympy: sympy/1.10.1 SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. tabix: tabix/0.2.6 Generic indexer for TAB-delimited genome position files tabixpp: tabixpp/1.1.0 C++ wrapper to tabix indexer taxator-tk: taxator-tk/1.3.3 A set of programs for the taxonomic analysis of nucleotide sequence data tbb: tbb/2020.3, tbb/2021.5.0 Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. tbl2asn: tbl2asn/20220427-linux64 Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank tcsh: tcsh/6.24.01 Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. tensorboard: tensorboard/2.10.0 TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs. tesseract: tesseract/5.3.0 Tesseract is an optical character recognition engine texinfo: texinfo/7.0.2 Texinfo is the official documentation format of the GNU project. texlive: texlive/20230313 TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated. tmux: tmux/3.5a tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached. torchvision: torchvision/0.13.1-CUDA-11.7.0, torchvision/0.13.1, ... Datasets, Transforms and Models specific to Computer Vision tqdm: tqdm/4.64.0 A fast, extensible progress bar for Python and CLI trimAl: trimAl/1.4.1 EVB, FEP and LIE simulator. typing-extensions: typing-extensions/4.3.0, typing-extensions/4.12.2 Typing Extensions – Backported and Experimental Type Hints for Python unifdef: unifdef/2.12 unifdef - selectively remove C preprocessor conditionals The unifdef utility selectively processes conditional C preprocessor and the additional text that they delimit, while otherwise leaving the file alone. unimelb-mf-clients: unimelb-mf-clients/current unimelb-mf-clients is a collection of command-line tools to transfer data to/from Mediaflux, the data management platform operated by Research Computing Services unrar: unrar/6.0.2 RAR is a powerful archive manager. utf8proc: utf8proc/2.7.0 utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. util-linux: util-linux/2.37, util-linux/2.38, util-linux/2.40 Set of Linux utilities vbz_compression: vbz_compression/1.0.2 VBZ compression HDF5 plugin for nanopolish vcfdist: vcfdist/2.3.2 vcfdist is a distance-based germline variant calling evaluation tool vcflib: vcflib/1.0.3 vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals. velocyto: velocyto/0.17.17 Velocyto is a library for the analysis of RNA velocity. versioneer: versioneer/0.28-Python-3.10.4 Easy VCS-based management of project version strings. vg: vg/1.54.0 Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of nodes, edges, and paths. virtualenv: virtualenv/20.23.1-Python-3.11.3 A tool for creating isolated virtual python environments. vt: vt/0.57721 A tool set for short variant discovery in genetic sequence data. wget: wget/1.21.3 GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. wgrib2: wgrib2/3.1.3 wgrib2 is a program to read/write grib2 files. wgsim: wgsim/20111017 Wgsim is a small tool for simulating sequence reads from a reference genome. wpebackend-fdo: wpebackend-fdo/1.14.1 WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. wrapt: wrapt/1.16.0-Python-3.11.3, wrapt/1.16.0 The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions. wxPython: wxPython/4.2.1-Python-3.11.3, wxPython/4.2.1 Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code. wxWidgets: wxWidgets/3.2.1 wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. x264: x264/20220620 x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. x265: x265/3.5 x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. xcb-proto: xcb-proto/1.17.0 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. xorg-macros: xorg-macros/1.19.3, xorg-macros/1.20.0 X.org macros utilities. xprop: xprop/1.2.5 The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. xproto: xproto/7.0.31 X protocol and ancillary headers xtb: xtb/6.5.1 xtb - An extended tight-binding semi-empirical program package. xxd: xxd/8.2.4220 xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files. yaff: yaff/1.6.0 Yaff stands for 'Yet another force field'. It is a pythonic force-field code. yaml-cpp: yaml-cpp/0.7.0, yaml-cpp/0.8.0 yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec zlib: zlib/1.2.12, zlib/1.2.13 zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. zstd: zstd/1.5.2 Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. ---------------------------------------------------------------------------- To learn more about a package execute: $ module spider Foo where "Foo" is the name of a module. To find detailed information about a particular package you must specify the version if there is more than one version: $ module spider Foo/11.1 ----------------------------------------------------------------------------