Software Modules on the Grace Cluster
ACES Software Modules FASTER Software Modules Grace Software Modules
(Last Updated: Dec 04, 2025)
| Name | Versions available | Description | Notes |
|---|---|---|---|
| 4TI2 | 4ti2/1.6.10 |
A software package for algebraic, geometric and combinatorial problems on linear spaces | |
| AAF | AAF/20171001 |
AAF constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. | |
| ABAQUS | ABAQUS/2025 ABAQUS/2024 ABAQUS/2023 ABAQUS/2022 ABAQUS/2021 ABAQUS/2020 |
Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. | HPRC Docs |
| ABSEIL | Abseil/20240722.0 Abseil/20240116.1 Abseil/20230125.3 Abseil/20230125.2 |
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. | |
| ABSL-PY | absl-py/2.1.0 absl-py/1.4.0 |
absl-py is a collection of Python library code for building Python applications. The code is collected from Google's own Python code base, and has been extensively tested and used in production. | |
| ABYSS | ABySS/2.3.7 |
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. | |
| ADAPTER_TRIM | adapter_trim/0.3.2 |
Removes 3' adapter from Illumina sequencing of small RNAs where read length is greater than the size of RNAs. | |
| ADEPT-2 | Adept-2/20231208 |
A combined array and automatic differentiation library in C++. | |
| AGAT | AGAT/1.4.2 |
AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format. | |
| AIOHTTP | aiohttp/3.8.5 |
Asynchronous HTTP client/server framework for asyncio and Python. | |
| ALEVIN-FRY | alevin-fry/0.9.0 |
alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding. | |
| ALLHIC | ALLHiC/0.9.14 |
Genome scaffolding based on Hi-C data | |
| ALPHAFOLD | AlphaFold/2.3.1-CUDA-11.7.0 |
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known | HPRC Docs |
| ALPHAFOLD3 | AlphaFold3/3.0.1 |
This module provides details on creating an AlphaFold3 jobscript. Run the following command to see how to create an AlphaFold3 jobscript: alphafold3jobscript --help . | |
| ALPHAPICKLE | AlphaPickle/1.4.1 |
ALPHAPICKLE is a programme for extracting the outputs of DeepMind's ALPHAFOLD protein prediction algorithm from the pickle (.pkl) file output. | |
| ALSA-LIB | alsa-lib/1.2.11 alsa-lib/1.2.9 |
The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. | |
| AMBER | Amber/24-NCCL-2.20.5-CUDA-12.4.1 Amber/22.4-AmberTools-22.5-CUDA-11.7.0 |
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. | HPRC Docs |
| AMRFINDERPLUS | AMRFinderPlus/4.0.23-2025-07-16.1 AMRFinderPlus/4.0.23 |
This software and the accompanying database are designed to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences. | |
| ANACONDA3 | Anaconda3/2024.02-1 Anaconda3/2023.09-0 Anaconda3/2021.11 Anaconda3/2021.05 |
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. | |
| ANGSD | angsd/0.940 |
Program for analysing NGS data. | |
| 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. | |
| ANNDATA | anndata/0.11.1 anndata/0.10.9 anndata/0.10.5.post1 |
anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray | |
| ANNOSINE | AnnoSINE/2024.01.16 |
SINE Annotation Tool for Plant Genomes | |
| ANNOVAR | ANNOVAR/20200607-Perl-5.36.0 |
ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). | |
| ANSYS | ANSYS/2025R2 ANSYS/2024R2 ANSYS/2023R2 ANSYS/2022R2 ANSYS/2022R1 |
Ansys offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires. | HPRC Docs |
| ANSYSEM | AnsysEM/2025R2 AnsysEM/2024R2 AnsysEM/2021R1 |
Ansys electromagnetic field simulation helps you design innovative electrical and electronic products faster and more cost-effectively. | |
| ANT | ant/1.10.14-Java-11 ant/1.10.12-Java-17 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. | |
| ANTLR | ANTLR/2.7.7-Java-17 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. | |
| ANY2FASTA | any2fasta/0.4.2 |
Convert various sequence formats to FASTA | |
| AOCL-BLAS | AOCL-BLAS/5.0 |
AOCL-BLAS is AMD's optimized version of BLAS targeted for AMD EPYC and Ryzen CPUs. | |
| APR | APR/1.7.4 APR/1.7.0 |
Apache Portable Runtime (APR) libraries. | |
| APR-UTIL | APR-util/1.6.1 |
Apache Portable Runtime (APR) util libraries. | |
| ARC-SV | ARC-SV/0.9.6-2025.01.09 |
ARC-SV: Automated Reconstruction of Complex Structural Variants | |
| ARCHR | ArchR/1.0.3-R-4.4.2 |
ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. | |
| ARCHSPEC | archspec/0.2.5 archspec/0.2.2 archspec/0.2.0 archspec/0.1.4 |
A library for detecting, labeling, and reasoning about microarchitectures | |
| ARCS | ARCS/1.2.7 |
Scaffolding genome sequence assemblies using linked or long read sequencing data | |
| ARGTABLE | argtable/2.13 |
Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. | |
| ARMADILLO | Armadillo/14.0.3 Armadillo/12.8.0 Armadillo/12.6.2 Armadillo/11.4.3 Armadillo/9.900.1 |
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. | |
| ARPACK-NG | arpack-ng/3.9.1 arpack-ng/3.9.0 arpack-ng/3.8.0 |
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | |
| ARROW-R | arrow-R/17.0.0.1-R-4.4.2 arrow-R/16.1.0-R-4.4.1 arrow-R/14.0.1-R-4.3.2 arrow-R/11.0.0.3-R-4.2.2 arrow-R/8.0.0-R-4.2.1 |
R interface to the Apache Arrow C++ library | |
| ASSEMBLYTICS | Assemblytics/1.2.1 |
Assemblytics: a web analytics tool for the detection of variants from an assembly | |
| ASSIMP | assimp/6.0.2 assimp/5.4.3 assimp/5.3.1 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. | |
| ASTER | ASTER/1.20.4 |
ASTER (Accurate Species Tree EstimatoR) is a family of optimization algorithms for species tree inference. | |
| ASTROPY | astropy/5.2.2 astropy/5.1.1 |
The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages. The Astropy community is committed to supporting diversity and inclusion. | |
| AT-SPI2-ATK | at-spi2-atk/2.38.0 |
AT-SPI 2 toolkit bridge | |
| AT-SPI2-CORE | at-spi2-core/2.54.0 at-spi2-core/2.50.0 at-spi2-core/2.49.91 at-spi2-core/2.46.0 at-spi2-core/2.44.1 |
Assistive Technology Service Provider Interface. | |
| 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. | |
| ATTR | attr/2.5.2 attr/2.5.1 |
Commands for Manipulating Filesystem Extended Attributes | |
| ATTRDICT3 | 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. | |
| AUGUSTUS | AUGUSTUS/3.5.0 |
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences | |
| AUTOCONF | Autoconf/2.72 Autoconf/2.71 Autoconf/2.69 |
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. | |
| AUTODOCK-GPU | AutoDock-GPU/1.5.3-CUDA-11.7.0 |
OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. 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. | |
| AUTOMAKE | Automake/1.17 Automake/1.16.5 Automake/1.16.4 Automake/1.16.3 Automake/1.16.1 |
Automake: GNU Standards-compliant Makefile generator | |
| AUTOTOOLS | Autotools/20240712 Autotools/20231222 Autotools/20220317 Autotools/20210726 Autotools/20210128 Autotools/20180311 |
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool | |
| AVOGADRO2 | Avogadro2/1.97.0-linux-x86_64 |
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | |
| AWSCLI | awscli/2.13.37 |
Universal Command Line Environment for AWS | |
| BAMTOOLS | BamTools/2.5.2 |
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. | |
| BANDAGE | Bandage/0.9.0 |
Bandage is a program for visualising de novo assembly graphs | |
| BAYSOR | Baysor/0.7.1 |
Baysor is a tool for performing cell segmentation on imaging-based spatial transcriptomics data. It optimizes segmentation considering the likelihood of transcriptional composition, size and shape of the cell. The approach can take into account nuclear or cytoplasm staining, however, can also perform segmentation based on the detected molecules alone. | |
| BAZEL | Bazel/6.5.0-Java-11 Bazel/6.3.1 Bazel/6.1.0 Bazel/5.1.1 |
Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. | |
| BAZELISK | bazelisk/1.25.0 |
Bazelisk is a wrapper for Bazel written in Go. | |
| BBMAP | BBMap/39.19 BBMap/39.13 BBMap/39.01 |
BBMap short read aligner, and other bioinformatic tools. | |
| BCBIO-GFF | bcbio-gff/0.7.1 bcbio-gff/0.7.0 |
Read and write Generic Feature Format (GFF) with Biopython integration. | |
| BCFTOOLS | BCFtools/1.19 BCFtools/1.18 BCFtools/1.17 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 | |
| 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. | |
| BCRYPT | bcrypt/4.1.3 bcrypt/4.1.1 bcrypt/4.0.1 bcrypt/3.2.0 |
Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt) | |
| BEAGLE-LIB | beagle-lib/4.0.1 beagle-lib/4.0.1-CUDA-12.1.1 beagle-lib/4.0.0 |
beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. | |
| BEAST | Beast/2.7.7 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/4.12.2 BeautifulSoup/4.11.1 BeautifulSoup/4.10.0 |
Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. | |
| BEDOPS | BEDOPS/2.4.42 |
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/2.31.1 BEDTools/2.31.0 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. | |
| BINDCRAFT | BindCraft/1.5.2-CUDA-12.1.1 |
Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. | |
| BINUTILS | binutils/2.44 binutils/2.42 binutils/2.40 binutils/2.39 binutils/2.38 binutils/2.37 binutils/2.36.1 binutils/2.35 binutils/2.34 binutils/2.32 |
binutils: GNU binary utilities | |
| BIO-EASEL | Bio-Easel/0.08 |
Easel is an ANSI C code library for computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies the Pfam protein families database, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. | |
| BIO-RESTRICTION | Bio-Restriction/1.7.3 |
Bio::Restriction Perl library | |
| 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. | |
| BIOINFOKIT | bioinfokit/2.1.4 |
The bioinfokit toolkit aimed to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments. | |
| BIOM-FORMAT | biom-format/2.1.16 biom-format/2.1.15 biom-format/2.1.14 |
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. | |
| 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/1.84 Biopython/1.83 Biopython/1.81 Biopython/1.79 Biopython/1.76-Python-2.7.18 |
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/3.7.6 Bison/3.7.1 Bison/3.5.3 Bison/3.3.2 |
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. | |
| BLAST+ | BLAST+/2.16.0 BLAST+/2.14.1 BLAST+/2.14.0 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. | |
| BLENDER | Blender/4.4.0-linux-x86_64-CUDA-12.1.1 Blender/4.0.1-linux-x86_64-CUDA-12.1.1 |
Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. | |
| BLIS | BLIS/1.1 BLIS/1.0 BLIS/0.9.0 BLIS/0.8.1 |
BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. | |
| BLOBTOOLKIT | BlobToolKit/4.4.5 |
BlobToolKit – Interactive quality assessment of genome assemblies. | |
| BLOBTOOLS | BlobTools/1.1.1 |
A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. | |
| BLOSC | Blosc/1.21.5 Blosc/1.21.3 |
Blosc, an extremely fast, multi-threaded, meta-compressor library | |
| BMTAGGER | bmtagger/3.101-Java-11 |
Best Match Tagger for removing human reads from metagenomics datasets | |
| BOKEH | bokeh/3.6.0 bokeh/3.4.1 bokeh/3.2.2 bokeh/2.4.3 |
Statistical and novel interactive HTML plots for Python | |
| BONSAI | Bonsai/0.5.1 |
Bonsai: Flexible Taxonomic Analysis and Extension | |
| BOOST | Boost/1.88.0 Boost/1.88.0-CDMS Boost/1.85.0 Boost/1.83.0 Boost/1.82.0 Boost/1.81.0 Boost/1.79.0 Boost/1.77.0 Boost/1.76.0 Boost/1.75.0 Boost/1.74.0 |
Boost provides free peer-reviewed portable C++ source libraries. | |
| BOOST.MPI | Boost.MPI/1.83.0 Boost.MPI/1.82.0 Boost.MPI/1.79.0 |
Boost provides free peer-reviewed portable C++ source libraries. | |
| BOOST.PYTHON | Boost.Python/1.88.0-CDMS Boost.Python/1.81.0 Boost.Python/1.79.0 |
Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. | |
| BOTO3 | boto3/1.35.36 boto3/1.34.51 boto3/1.28.70 |
Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python, which allows Python developers to write software that makes use of services like Amazon S3 and Amazon EC2. | |
| 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 | Bowtie2/2.5.4 Bowtie2/2.5.1 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. | |
| BPP | bpp/4.7.0 |
Bayesian analysis of genomic sequence data under the multispecies coalescent model. | |
| BRACKEN | Bracken/3.1 |
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. | |
| BRAKER | BRAKER/3.0.8 BRAKER/3.0.8-long_reads BRAKER/3.0.7 BRAKER/3.0.7-container |
BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes. | |
| BROTLI | Brotli/1.1.0 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. | |
| BROTLI-PYTHON | Brotli-python/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. | |
| BS-SNPER | BS-Snper/1.0 |
BS-SNPer is an ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM/SAM format using approximate Bayesian modeling. | |
| BTLLIB | btllib/1.7.0 btllib/1.6.2 btllib/1.4.10 |
Bioinformatics Technology Lab common code library | |
| BUSCO | BUSCO/6.0.0 BUSCO/5.7.1 |
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | |
| BWA | BWA/0.7.18 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. | |
| BWA-MEM2 | bwa-mem2/2.2.1-Linux64 |
Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. | |
| BX-PYTHON | bx-python/0.11.0 bx-python/0.9.0 |
The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses. | |
| 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/1.27.0 c-ares/1.19.1 |
c-ares is a C library for asynchronous DNS requests (including name resolves) | |
| CACTUS | Cactus/2.9.1 |
Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit. | |
| 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. | |
| CAPNPROTO | CapnProto/1.0.1 CapnProto/0.10.2 |
Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. | |
| CAPSTONE | Capstone/5.0.3 |
Capstone disassembly/disassembler framework for ARM, ARM64 (ARMv8), Alpha, BPF, Ethereum VM, HPPA, LoongArch, M68K, M680X, Mips, MOS65XX, PPC, RISC-V(rv32G/rv64G), SH, Sparc, SystemZ, TMS320C64X, TriCore, Webassembly, XCore and X86. | |
| CASTOR | castor/1.7.11 |
Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. | |
| CATCH | CATCH/1.5.2 |
Compact Aggregation of Targets for Comprehensive Hybridization. CATCH is a Python package for designing probe sets to use for nucleic acid capture of diverse sequence. | |
| CATCH2 | Catch2/2.13.10 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 | |
| CATH-RESOLVE-HITS | cath-resolve-hits/0.16.2-linux-x86_64 |
Collapse a list of domain matches to your query sequence(s) down to the non-overlapping subset (ie domain architecture) that maximises the sum of the hits' scores. | |
| CAT_PACK | CAT_pack/6.0.1 |
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs / bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against a protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately. | |
| CBC | Cbc/2.10.12 Cbc/2.10.11 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. | |
| CCACHE | ccache/4.9 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 | |
| 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 | |
| CDDLIB | cddlib/0.94m |
An efficient implementation of the Double Description Method | |
| CDNA_CUPCAKE | cDNA_Cupcake/29.0.0 |
cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. | |
| CDO | CDO/2.4.4 |
CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. | |
| CELLRANGER-ARC | CellRanger-ARC/2.0.2 |
Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression. | |
| CELLSNP-LITE | cellsnp-lite/1.2.3 |
Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. | |
| CENTIER | CentIER/2.0 |
CentIER is a bioinformatics tool for identifying and annotating centromere regions of the genome that can be accurately identified. | |
| CEREAL | Cereal/1.3.2 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. | |
| CERES-SOLVER | Ceres-Solver/2.2.0 |
Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems | |
| CESM-DEPS | CESM-deps/2 |
CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. | |
| CFFI | cffi/1.17.1 cffi/1.16.0 cffi/1.15.1 cffi/1.14.6 cffi/1.14.5 cffi/1.14.3 |
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. | |
| CFITSIO | CFITSIO/4.4.1 CFITSIO/4.3.1 CFITSIO/4.3.0 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. | |
| CFOUR | CFOUR/2.1-GNU-OpenBLAS CFOUR/2.1-GNU-MKL |
CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. CFOUR is distributed under a non-commercial license. Users must provide confirmation of a signed license agreement with the CFOUR team. | |
| CGAL | CGAL/5.6.1 CGAL/5.6 CGAL/5.5.2 CGAL/4.14.3 |
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. | |
| CGL | Cgl/0.60.8 Cgl/0.60.7 |
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. | |
| CGMLSTFINDER | cgMLSTFinder/1.3.0 |
Core genome Multi-Locus Sequence Typing | |
| CGNS | CGNS/4.5.0 |
The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. | |
| CHARMM | CHARMM/c49b2-omm CHARMM/c46b2charmm/45b1-medium charmm/45b1-medium-serial charmm/45b1-huge charmm/45b1-huge-serial |
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm (CHARMM lite) provides all the functionality of CHARMM except its performance enhancements. | HPRC Docs |
| CHECK | check/0.15.2 |
A unit testing framework for C. | |
| CHECKM | 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 | CheckM2/1.1.0 CheckM2/1.0.2 |
Assessing the quality of metagenome-derived genome bins using machine learning | |
| CHECKV | checkv/1.0.3 |
CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. | |
| CHIMERAX | ChimeraX/1.7.1 |
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. | |
| CHROMVARMOTIFS | chromVARmotifs/0.2.0-R-4.4.2 |
The goal of chromVARmotifs is to make it easy to use several different motif collections in R, particularly for use with motifmatchr and chromVAR packages. | |
| CIMFOMFA | cimfomfa/22.273 |
This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. Both understandably and regrettably I chose long ago to make it C-string-compatible, hence nul bytes may not be part of a string. At some point I hope to rectify this, perhaps unrealistically. | |
| 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. | |
| CISTEM | cisTEM/1.0.0-beta-Linux64 |
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | |
| CLANG | Clang/18.1.8 Clang/17.0.6 Clang/17.0.0_20230515-CUDA-12.1.1 Clang/16.0.6 Clang/13.0.1 |
C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. | |
| CLHEP | CLHEP/2.4.7.1 |
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. | |
| CLP | Clp/1.17.10 Clp/1.17.9 Clp/1.17.8 |
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 | |
| CLUSTALW2 | ClustalW2/2.1 |
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. | |
| CMAKE | CMake/3.31.3 CMake/3.29.3 CMake/3.27.6 CMake/3.26.3 CMake/3.24.3 CMake/3.23.1 CMake/3.22.1 CMake/3.21.1 CMake/3.20.1 CMake/3.18.4 CMake/3.16.4 CMake/3.15.3 CMake/3.12.1 |
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | |
| CMG | CMG/2023.30 |
CMG provides reservoir simulation software. | |
| CMSEQ | CMSeq/1.0.4 |
CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus. | |
| COCOALIB | CoCoALib/0.99850 |
CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra. | |
| COINUTILS | CoinUtils/2.11.12 CoinUtils/2.11.10 CoinUtils/2.11.9 |
CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. | |
| COLMAP | COLMAP/3.11.1-CUDA-12.3.0 COLMAP/3.8 |
COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface | |
| COMPLEASM | Compleasm/0.2.7 |
Copleasm: a faster and more accurate reimplementation of BUSCO. | |
| CONAN | conan/1.58.0 |
Decentralized, open-source (MIT), C/C++ package manager. | |
| CONCURRENTQUEUE | concurrentqueue/1.0.4 |
A Persistent Key-Value Store for Flash and RAM Storage | |
| CONFIGURABLE-HTTP-PROXY | configurable-http-proxy/4.5.6 |
HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server. | |
| COOLER | cooler/0.9.1 |
Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices. | |
| COORDGENLIBS | CoordgenLibs/3.0.1 |
Schrodinger-developed 2D Coordinate Generation | |
| COREUTILS | Coreutils/9.1 |
The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. | |
| COVERM | CoverM/0.7.0 CoverM/0.7.0-dashing-1.0.3 CoverM/0.6.1 |
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. | |
| CP2K-INPUT-TOOLS | cp2k-input-tools/0.9.1 |
Fully validating pure-python CP2K input file parsers including preprocessing capabilities | |
| CPIO | cpio/2.15 |
The cpio package contains tools for archiving. | |
| CPPY | cppy/1.3.1 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. | |
| CPPYY | cppyy/3.1.2 |
cppyy is an automatic, run-time, Python-C++ bindings generator, for calling C++ from Python and Python from C++. | |
| CRYODRGN | cryoDRGN/2.3.0-CUDA-11.7.0 |
cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction. CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume. | |
| CRYOSPARC | CryoSPARC/4.7.1 CryoSPARC/4.5.1 |
This module provides details running CryoSPARC on the Grace Open OnDemand portal. Use the Grace Open OnDemand portal to launch the CryoSPARC Interactive App. | |
| CRYPTOGRAPHY | cryptography/44.0.2 cryptography/42.0.8 cryptography/41.0.5 cryptography/41.0.1 cryptography/3.4.7 cryptography/3.1.1 |
cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. | |
| CTFFIND | ctffind/4.1.14 |
Program for finding CTFs of electron micrographs. | |
| CUDA | CUDA/12.9.0 CUDA/12.8.0 CUDA/12.6.0 CUDA/12.4.1 CUDA/12.4.0 CUDA/12.3.2 CUDA/12.3.0 CUDA/12.2.2 CUDA/12.2.0 CUDA/12.1.1 CUDA/11.8.0 CUDA/11.7.0 CUDA/11.4.1 CUDA/11.3.1 CUDA/10.1.243 CUDA/10.0.130 |
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. | |
| CUDACORE | CUDAcore/11.1.1 |
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. | |
| CUDA_PYTHON | cuda_python/0.2.0 |
CUDA Python is the home for accessing NVIDIA’s CUDA platform from Python. | |
| CUDNN | cuDNN/9.5.0.50-CUDA-12.6.0 cuDNN/8.9.2.26-CUDA-12.1.1 cuDNN/8.5.0.96-CUDA-11.7.0 cuDNN/8.4.1.50-CUDA-11.7.0 cuDNN/8.2.2.26-CUDA-11.4.1 cuDNN/8.0.4.30-CUDA-11.1.1 |
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. | |
| CUFFLINKS | Cufflinks/20190706 |
Transcript assembly, differential expression, and differential regulation for RNA-Seq | |
| CUNIT | CUnit/2.1-3 |
Automated testing framework for C. | |
| CUSPARSELT | cuSPARSELt/0.6.0.6-CUDA-12.1.1 |
NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix | |
| CUTADAPT | cutadapt/5.0 cutadapt/4.9 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. | |
| CUTENSOR | cuTENSOR/2.0.1.2-CUDA-12.1.1 |
The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations. | |
| CVXOPT | CVXOPT/1.3.2 CVXOPT/1.3.1 |
CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language. | |
| CYTHON | Cython/3.1.1 Cython/3.0.10 Cython/3.0.8 Cython/3.0.7 Cython/0.29.37 Cython/0.29.33 Cython/0.29.24 Cython/0.29.23 Cython/0.29.21 Cython/0.27.3-Python-2.7.18 |
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). | |
| DALIGNER | DALIGNER/20240118 |
Daligner: The Dazzler "Overlap" Module | |
| DAMASK | DAMASK/3.0.2 |
DAMASK® is a unified multi-physics crystal plasticity simulation package. The solution of continuum mechanical boundary value problems requires a constitutive response that connects deformation and stress at each material point. This problem is solved in DAMASK on the basis of crystal plasticity using a variety of constitutive models and homogenization approaches. However, treating mechanics in isolation is no longer sufficient to study emergent advanced high-strength materials. In these materials, deformation happens interrelated with displacive phase transformation, significant heating, and potential damage evolution. Therefore, DAMASK is capable of handling multi-physics problems. Following a modular approach, additional field equations are solved in a fully coupled way using a staggered approach. | |
| DAMASK-GRID | DAMASK-GRID/3.0.2 |
DAMASK® is a unified multi-physics crystal plasticity simulation package. The solution of continuum mechanical boundary value problems requires a constitutive response that connects deformation and stress at each material point. This problem is solved in DAMASK on the basis of crystal plasticity using a variety of constitutive models and homogenization approaches. However, treating mechanics in isolation is no longer sufficient to study emergent advanced high-strength materials. In these materials, deformation happens interrelated with displacive phase transformation, significant heating, and potential damage evolution. Therefore, DAMASK is capable of handling multi-physics problems. Following a modular approach, additional field equations are solved in a fully coupled way using a staggered approach. | |
| DAMASK-MESH | DAMASK-MESH/3.0.2 |
DAMASK® is a unified multi-physics crystal plasticity simulation package. The solution of continuum mechanical boundary value problems requires a constitutive response that connects deformation and stress at each material point. This problem is solved in DAMASK on the basis of crystal plasticity using a variety of constitutive models and homogenization approaches. However, treating mechanics in isolation is no longer sufficient to study emergent advanced high-strength materials. In these materials, deformation happens interrelated with displacive phase transformation, significant heating, and potential damage evolution. Therefore, DAMASK is capable of handling multi-physics problems. Following a modular approach, additional field equations are solved in a fully coupled way using a staggered approach. | |
| DASK | dask/2024.9.1 dask/2024.5.1 dask/2023.9.2 dask/2022.10.0 |
Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. | |
| DASK-ML | Dask-ML/2024.4.4 |
Dask-ML provides scalable machine learning in Python using Dask alongside popular machine learning libraries like Scikit-Learn, XGBoost, and others. | |
| DAS_TOOL | DAS_Tool/1.1.7-R-4.4.1 |
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. | |
| DATES | DATES/20220112 |
DATES (Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Narasimhan, Patterson et al. 2018 | |
| DAZZ_DB | DAZZ_DB/20250217 |
The Dazzler Database Library | |
| DB | DB/18.1.40 DB/18.1.32 |
Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. | |
| DBUS | DBus/1.16.2 DBus/1.15.8 DBus/1.15.4 DBus/1.15.2 DBus/1.14.0 DBus/1.13.18 |
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. | |
| DB_FILE | DB_File/1.859 DB_File/1.858 |
Perl5 access to Berkeley DB version 1.x. | |
| DECHAT | DeChat/1.0.1 |
Error correction is the canonical first step in long-read sequencing data analysis. Nanopore R10 reads have error rates below 2%. We introduce DeChat, a novel approach specifically designed for Nanopore R10 reads. DeChat enables repeat- and haplotype-aware error correction, leveraging the strengths of both de Bruijn graphs and variant-aware multiple sequence alignment to create a synergistic approach. This approach avoids read overcorrection, ensuring that variants in repeats and haplotypes are preserved while sequencing errors are accurately corrected. DeChat can use HIFi or NGS to correct ONT now. Dechat is implemented with C++. | |
| DEEPDIFF | deepdiff/6.7.1 |
DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. | |
| DEEPSPACE | DEEPSPACE/1.0a |
DEEPSPACE is an annotation-free version of GENESPACE. Feed it the genome assemblies and it produces the standard GENESPACE graphical outputs (dotplots, riparian). | |
| 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. | |
| DELLY | Delly/1.1.6 |
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. | |
| DELTALAKE | DeltaLake/0.25.5 DeltaLake/0.15.1 |
Native Delta Lake Python binding based on delta-rs with Pandas integration. The Delta Lake project aims to unlock the power of the Deltalake for as many users and projects as possible by providing native low-level APIs aimed at developers and integrators, as well as a high-level operations API that lets you query, inspect, and operate your Delta Lake with ease. | |
| DENDROPY | DendroPy/5.0.1 DendroPy/4.6.1 DendroPy/4.5.2 |
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. | |
| DESMOND | Desmond/2024-4 Desmond/2023-2 Desmond/2022-1 Desmond/2021-1 Desmond/2020-1 |
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on NVIDIA GPUs. | HPRC Docs |
| DIAMOND | DIAMOND/2.1.11 DIAMOND/2.1.9 DIAMOND/2.1.8 DIAMOND/2.1.0 |
Accelerated BLAST compatible local sequence aligner | |
| DIFFDOCK | diffdock/1.1.3 |
Implementation of DiffDock, state-of-the-art method for molecular docking. | |
| DILL | dill/0.3.9 dill/0.3.8 dill/0.3.7 dill/0.3.6 |
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. | |
| DJVULIBRE | DjVuLibre/3.5.28 |
DjVuLibre is an open source (GPL'ed) implementation of DjVu, including viewers, browser plugins, decoders, simple encoders, and utilities. | |
| DM-TREE | dm-tree/0.1.8 |
dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure. | |
| 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. | |
| DOLFINX | DOLFINx/0.9.0 |
DOLFINx is the computational environment of FEniCSx and implements the FEniCS Problem Solving Environment in C++ and Python. DOLFINx is a new version of DOLFIN and is actively developed. | |
| DORADO | Dorado/0.6.1-Linux64 Dorado/0.0.3-Linux64dorado/0.9.1-CUDA-12.1.1 |
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | |
| DOTNET-CORE | dotNET-Core/8.0.411 |
.NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime. | |
| DOUBLE-CONVERSION | double-conversion/3.3.1 double-conversion/3.3.0 double-conversion/3.2.1 double-conversion/3.2.0 double-conversion/3.1.5 |
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. | |
| DOXYGEN | Doxygen/1.14.0 Doxygen/1.11.0 Doxygen/1.9.8 Doxygen/1.9.7 Doxygen/1.9.5 Doxygen/1.9.4 Doxygen/1.9.1 |
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. | |
| DRAM | DRAM/1.5.0 |
DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the user), UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database as well as custom user databases. | |
| 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. | |
| DTCMP | dtcmp/1.1.5 |
The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined comparison operations to compare the values of two items which can be arbitrary MPI datatypes. Using these comparison operations, the library provides various routines for manipulating data, which may be distributed over the processes of an MPI communicator. | |
| DUPLEX-TOOLS | duplex-tools/0.3.3 |
Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for recovering simplex basecalls from incorrectly concatenated pairs. | |
| E-ANTIC | E-ANTIC/2.0.2 |
E-ANTIC is a C/C++ library to deal with real embedded number fields built on top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as possible exact arithmetic operations and comparisons. | |
| EASYBUILD | EasyBuild/5.1.2 EasyBuild/5.1.1 EasyBuild/5.1.0 EasyBuild/5.0.0 EasyBuild/4.9.4 |
EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. | |
| EASYBUILD-GRACE | EasyBuild-grace/0 |
EasyBuild environment variables for building system software in /tmp and installing in /sw/eb on grace.hprc.tamu.edu | |
| EASYBUILD-GRACE-SCRATCH | EasyBuild-grace-SCRATCH/0 |
User EasyBuild environment for grace.hprc.tamu.edu in $SCRATCH/eb | |
| EASYBUILD-GRACE-TMP | EasyBuild-grace-tmp/0 |
EasyBuild environment variables for building in /tmp and installing in /sw/eb on grace.hprc.tamu.edu | |
| ECBUILD | ecBuild/3.8.5 |
A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems | |
| ECCODES | ecCodes/2.38.3 |
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). | |
| ECLIPSE | ECLIPSE/2025.2 ECLIPSE/2022.4 |
The ECLIPSE industry-reference simulator offers the industry’s most complete and robust set of numerical solutions for fast and accurate prediction of dynamic behavior for all types of reservoirs and development schemes. The ECLIPSE simulator has been the benchmark for commercial reservoir simulation for more than 25 years thanks to its extensive capabilities, robustness, speed, parallel scalability, and unmatched platform coverage. | |
| EDEM | EDEM/2024.1 |
Altair EDEM | |
| EDIRECT | EDirect/23.5.20250218 |
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. | |
| EDTA | EDTA/2.2.2-CUDA-12.1.1 |
This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries. | |
| EGAPX | EGAPx/0.4.1-alpha EGAPx/0.3.2-alpha |
EGAPx is the publicly accessible version of the updated NCBI Eukaryotic Genome Annotation Pipeline. | |
| EGGNOG-MAPPER | eggnog-mapper/2.1.12 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. | |
| EIGEN | Eigen/3.4.0 Eigen/3.3.9 Eigen/3.3.7 |
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | |
| EINOPS | einops/0.8.0 einops/0.7.0 einops/0.4.1 |
Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others. | |
| ELFUTILS | elfutils/0.189 elfutils/0.187 |
The elfutils project provides libraries and tools for ELF files and DWARF data. | |
| ELPA | ELPA/2024.05.001 ELPA/2023.05.001 ELPA/2022.05.001 ELPA/2021.11.001 |
Eigenvalue SoLvers for Petaflop-Applications. | |
| EMACS | Emacs/28.2 |
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. | |
| EMAN2 | EMAN2/2.91 |
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. | |
| 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. | |
| EMCEE | emcee/3.1.4 |
Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet! | |
| EMU | Emu/3.5.4 |
Emu: species-level taxonomic abundance for full-length 16S reads | |
| ENCHANT-2 | enchant-2/2.6.5 |
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. | |
| ENTAP | EnTAP/2.3.0 |
EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. | |
| EPA-NG | EPA-ng/0.3.8 |
EPA-ng - Fast, parallel, highly accurate Maximum Likelihood Phylogenetic Placement, by the team behind RAxML(-ng) | |
| ESMF | ESMF/8.7.0 ESMF/8.6.1 ESMF/8.6.0 ESMF/8.3.0 ESMF/8.1.1 |
The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. | |
| ETE | ETE/3.1.3 ETE/3.1.2 |
A Python framework for the analysis and visualization of trees | |
| EXONERATE | Exonerate/2.4.0 |
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. | |
| EXPAT | expat/2.6.4 expat/2.6.2 expat/2.5.0 expat/2.4.9 expat/2.4.8 expat/2.4.1 expat/2.2.9 |
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/0.2.1 expecttest/0.1.5 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. | |
| FASTAHACK | fastahack/1.0.0 |
Utilities for indexing and sequence extraction from FASTA files. | |
| FASTANI | FastANI/1.34 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/2.1.6.3 |
FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. | |
| FASTP | fastp/0.23.4 |
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-SCREEN | FastQ-Screen/0.15.1 |
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. | |
| FASTQC | FastQC/0.12.1-Java-11 FastQC/0.11.9-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. | |
| FASTSTRUCTURE | fastStructure/1.0 |
fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm on a test simulated genotype dataset. | |
| 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. | |
| FEBIO | FEBio/4.10 FEBio/4.6 |
FEBio is a nonlinear finite element (FE) solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models and boundary conditions that are relevant to many research areas in biomechanics. All features can be used together seamlessly, giving the user a powerful tool for solving 3D problems in computational biomechanics. | |
| FEELNC | FEELnc/0.2 |
FlExible Extraction of Long non-coding RNAs This document is intended to give a technical description of the FEELnc pipeline in order to annotate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (either with or without a reference genome). For a more general overview of lncRNAs annotation using RNASeq and FEELnc specific advantages, you could point to the FEELnc paper. | |
| FEMZIP-L | FEMZIP-L/10.73 |
FEMZIP-L is a data compression software package for LS-DYNA result files - Homepage: http://www.sidact.com/femzip-crash.html | |
| FERMI-LITE | fermi-lite/20190320 |
Standalone C library for assembling Illumina short reads in small regions. | |
| FFMPEG | FFmpeg/7.1.1 FFmpeg/7.0.2 FFmpeg/6.0 FFmpeg/5.1.2 FFmpeg/4.4.2 FFmpeg/4.3.2 |
A complete, cross-platform solution to record, convert and stream audio and video. | |
| FFNVCODEC | ffnvcodec/13.0.19.0 ffnvcodec/12.2.72.0 ffnvcodec/12.1.14.0 ffnvcodec/12.0.16.0 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). | |
| 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. | |
| FIJI | Fiji/2.14.0-Java-11 Fiji/2.14.0-Java-11-plugins |
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 | |
| FILE | file/5.46 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. | |
| FIO | fio/3.38 |
Flexible I/O tester | |
| FIREFOX | Firefox/138.0.3 Firefox/136.0.2 |
Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks. | |
| FIXCHR | fixchr/2024.11.21 |
This package selects homologous chromosomes between two genomes by comparing whole-genome alignments between them. Additionally, it generates dotplots for quick checking of the output. | |
| FLAC | FLAC/1.4.3 FLAC/1.4.2 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/1.9.2 |
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. | |
| FLATBUFFERS | flatbuffers/24.3.25 flatbuffers/23.5.26 flatbuffers/23.1.4 flatbuffers/2.0.7 |
FlatBuffers: Memory Efficient Serialization Library | |
| FLATBUFFERS-PYTHON | flatbuffers-python/24.3.25 flatbuffers-python/23.5.26 flatbuffers-python/23.1.4 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. | |
| FLEXIBLAS | FlexiBLAS/3.4.5 FlexiBLAS/3.4.4 FlexiBLAS/3.3.1 FlexiBLAS/3.2.1 FlexiBLAS/3.2.0 FlexiBLAS/3.0.4 |
FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. | |
| FLINT | FLINT/3.1.1 |
FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. | |
| FLIT | flit/3.10.1 flit/3.9.0 flit/3.3.0 flit/3.2.0 flit/3.0.0 |
A simple packaging tool for simple packages. | |
| FLOOK | flook/0.8.4 |
The fortran-Lua-hook library. | |
| FLTK | FLTK/1.4.4 FLTK/1.4.3 FLTK/1.3.11 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. | |
| FLYE | Flye/2.9.5 Flye/2.9.4 Flye/2.9.2 Flye/2.6 |
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. | |
| FONTCONFIG | fontconfig/2.16.2 fontconfig/2.15.0 fontconfig/2.14.2 fontconfig/2.14.1 fontconfig/2.14.0 fontconfig/2.13.94 fontconfig/2.13.93 |
Fontconfig is a library designed to provide system-wide font configuration, customization and application access. | |
| FONTTOOLS | fonttools/4.58.4 fonttools/4.53.1 |
fontTools is a library for manipulating fonts, written in Python. The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats. | |
| FOSS | foss/2025a foss/2024a foss/2023b foss/2023a foss/2022b foss/2022a foss/2021b foss/2021a foss/2020a |
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | |
| FRAGGENESCAN | FragGeneScan/1.31 |
FragGeneScan is an application for finding (fragmented) genes in short reads. | |
| FREALIGN | FREALIGN/9.11_151031 |
Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. | |
| FREEBAYES | freebayes/1.3.7-R-4.3.2 |
Bayesian haplotype-based genetic polymorphism discovery and genotyping. | |
| FREEGLUT | freeglut/3.6.0 freeglut/3.4.0 |
freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. | |
| 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. | |
| FREETYPE | freetype/2.13.3 freetype/2.13.2 freetype/2.13.0 freetype/2.12.1 freetype/2.11.0 freetype/2.10.4 |
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. | |
| FREEXL | FreeXL/2.0.0 |
FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. | |
| FRIBIDI | FriBidi/1.0.16 FriBidi/1.0.15 FriBidi/1.0.13 FriBidi/1.0.12 FriBidi/1.0.10 |
The Free Implementation of the Unicode Bidirectional Algorithm. | |
| FSOM | fsom/20151117 |
A tiny C library for managing SOM (Self-Organizing Maps) neural networks. | |
| G2CLIB | g2clib/1.6.3 |
Library contains GRIB2 encoder/decoder ('C' version). | |
| G2LIB | g2lib/3.2.0 |
Library contains GRIB2 encoder/decoder and search/indexing routines. | |
| GAMS | GAMS/49.2 |
The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. It consists of a language compiler and a stable of integrated high-performance solvers. GAMS is tailored for complex, large scale modeling applications, and allows you to build large maintainable models that can be adapted quickly to new situations. traditional programming languages such as C, C++, and Fortran. | HPRC Docs |
| GAP | gap/4.13.0 gap/1.6 gap/1.5-3 |
GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. | |
| GAPPA | gappa/0.8.5 |
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. | |
| GATE | GATE/9.4 |
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/4.6.1.0-Java-17 GATK/4.6.0.0-Java-17 GATK/4.5.0.0-Java-17 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. | |
| GAUSSIAN | Gaussian/g16_C01 Gaussian/g16_B01 |
Gaussian 16 is the latest version of the Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Gaussian 16 provides a wide-ranging suite of the most advanced modeling capabilities available. You can use it to investigate the real-world chemical problems that interest you, in all of their complexity, even on modest computer hardware. Homepage: http://gaussian.com/ | HPRC Docs |
| GBSX | GBSX/1.3 |
GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments Genotyping by Sequencing is an emerging technology for cost effective variant discovery and genotyping. However, current analysis tools do not fulfill all experimental design and analysis needs. GBSX is a package of tools to first aid in experimental design, including choice of enzymes and barcode design. Secondly, it provides a first analysis step to demultiplex samples using in-line barcodes, providing fastq files that can easily be plugged into existing variant analysis pipelines. | |
| GC | gc/8.2.4 |
The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. | |
| GCC | GCC/14.3.0 GCC/14.2.0 GCC/13.3.0 GCC/13.2.0 GCC/12.3.0 GCC/12.2.0 GCC/11.3.0 GCC/11.2.0 GCC/10.3.0 GCC/10.2.0 GCC/9.3.0 GCC/8.3.0 |
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/14.3.0 GCCcore/14.2.0 GCCcore/13.3.0 GCCcore/13.2.0 GCCcore/12.3.0 GCCcore/12.2.0 GCCcore/11.3.0 GCCcore/11.2.0 GCCcore/10.3.0 GCCcore/10.2.0 GCCcore/9.3.0 GCCcore/8.3.0 |
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,...). | |
| GCLOUD | gcloud/472.0.0 |
Libraries and tools for interacting with Google Cloud products and services. | |
| 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). | |
| GD | GD/2.75 |
GD.pm - Interface to Gd Graphics Library | |
| GDAL | GDAL/3.10.0 GDAL/3.9.0 GDAL/3.7.1 GDAL/3.6.2 GDAL/3.5.0 GDAL/3.3.0 |
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/14.2 GDB/13.2 GDB/12.1 |
The GNU Project Debugger | |
| GDK-PIXBUF | Gdk-Pixbuf/2.42.12 Gdk-Pixbuf/2.42.11 Gdk-Pixbuf/2.42.10 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. | |
| GDOWN | gdown/5.2.0 gdown/4.7.1 |
Google Drive Public File Downloader when curl/wget Fails | |
| GDRCOPY | GDRCopy/2.4.1 GDRCopy/2.4 GDRCopy/2.3.1 GDRCopy/2.3 |
A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. | |
| GEANT4 | Geant4/11.2.2 |
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/11.2 |
Datasets for Geant4. | |
| GEMMA | GEMMA/0.98.5 |
Genome-wide Efficient Mixed Model Association | |
| GENEMARK-ES | GeneMark-ES/4.33 |
GeneMark-ES - Gene Prediction in Eukaryotes. Unsupervised training is an important feature of the GeneMark-ES algorithm that identifies protein coding genes in eukaryotic genomes. This is the only eukaryotic gene finder that can perform gene prediction without curated training sets. | |
| GENEMARK-ET | GeneMark-ET/4.72 GeneMark-ET/4.71 |
Eukaryotic gene prediction suite with automatic training | |
| GENEMARK-ETP | GeneMark-ETP/1.02 |
Gene finding in eukaryotic genomes by GeneMark-ETP | |
| GENEMARKS | GeneMarkS/4.30 |
GeneMarkS - Gene Prediction in Prokaryotes. | |
| GENERICREPEATFINDER | GenericRepeatFinder/1.0.2 |
Generic Repeat Finder (GRF) is a C++ program package for detecting terminal inverted repeats (TIRs), terminal direct repeats (TDRs), interspersed repeats, miniature inverted repeat transposable elements (MITEs), and long terminal repeat (LTR) transposons in genomes. | |
| GENOMETHREADER | GenomeThreader/1.7.3-Linux_x86_64-64bit |
GenomeThreader is a software tool to compute gene structure predictions. | |
| GENOMETOOLS | GenomeTools/1.6.5 GenomeTools/1.6.2 |
A comprehensive software library for efficient processing of structured genome annotations. | |
| GEOS | GEOS/3.12.2 GEOS/3.12.1 GEOS/3.12.0 GEOS/3.11.1 GEOS/3.10.3 GEOS/3.9.1 |
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) | |
| GETORGANELLE | GetOrganelle/1.7.7.1 |
This toolkit assemblies organelle genome from genomic skimming data. | |
| GETTEXT | gettext/0.24 gettext/0.22.5 gettext/0.22 gettext/0.21.1 gettext/0.21 gettext/0.20.1 |
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 | |
| GFATOOLS | gfatools/0.5 |
gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. | |
| GFBF | gfbf/2025a gfbf/2024a gfbf/2023b gfbf/2023a gfbf/2022b 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. | |
| GFFUTILS | gffutils/0.13 |
Gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. | |
| 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. | |
| GH | gh/2.52.0 gh/1.4.1 gh/1.4.0 |
GitHub’s official command line tool | |
| GHOSTSCRIPT | Ghostscript/10.03.1 Ghostscript/10.02.1 Ghostscript/10.01.2 Ghostscript/10.0.0 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. | |
| GIFLIB | giflib/5.2.2 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-LFS | git-lfs/3.5.1 git-lfs/3.2.0 |
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 | |
| GITPYTHON | GitPython/3.1.43 GitPython/3.1.42 GitPython/3.1.40 GitPython/3.1.31 GitPython/3.1.27 |
GitPython is a python library used to interact with Git repositories | |
| GL2PS | GL2PS/1.4.2 |
GL2PS: an OpenGL to PostScript printing library | |
| GLEW | glew/2.2.0-osmesa glew/2.2.0-glx 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 | GLib/2.85.1 GLib/2.80.4 GLib/2.78.1 GLib/2.77.1 GLib/2.75.0 GLib/2.72.1 GLib/2.68.2 |
GLib is one of the base libraries of the GTK+ project | |
| GLIB-NETWORKING | glib-networking/2.72.1 |
Network extensions for GLib | |
| GLIBMM | GLibmm/2.77.0 |
C++ bindings for Glib | |
| GLOBALARRAYS | GlobalArrays/5.8.2 GlobalArrays/5.8.1 |
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model | |
| GLOBUS-CLI | Globus-CLI/3.34.0 |
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. | |
| GLOG | glog/0.6.0 |
A C++ implementation of the Google logging module. | |
| 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. | |
| GLSLANG-SPIRV | glslang-SPIRV/15.3.0 |
Glslang is the official reference compiler front end for the OpenGL ES and OpenGL shading languages. It implements a strict interpretation of the specifications for these languages. It is open and free for anyone to use, either from a command line or programmatically. The OpenGL and OpenGL ES working groups are committed to maintaining consistency between the reference compiler and the corresponding shading language specifications. | |
| GMAP-GSNAP | GMAP-GSNAP/2024-09-18 GMAP-GSNAP/2023-04-20 GMAP-GSNAP/2023-02-17 |
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program | |
| GMPY2 | gmpy2/2.2.0 gmpy2/2.1.5 gmpy2/2.1.2 |
GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x | |
| GNINA | gnina/1.3 gnina/1.1 |
gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina. | |
| GNUPG-BUNDLE | gnupg-bundle/20240306 |
GnuPG — The Universal Crypto Engine | |
| GNUPLOT | gnuplot/6.0.1 gnuplot/5.4.8 gnuplot/5.4.4 gnuplot/5.4.2 gnuplot/4.6.0 |
Portable interactive, function plotting utility | |
| 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. | |
| GOBJECT-INTROSPECTION | GObject-Introspection/1.84.0 GObject-Introspection/1.80.1 GObject-Introspection/1.78.1 GObject-Introspection/1.76.1 GObject-Introspection/1.74.0 GObject-Introspection/1.72.0 GObject-Introspection/1.68.0 |
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. | |
| GOMPI | gompi/2025a gompi/2024a gompi/2023b gompi/2023a gompi/2022b gompi/2022a gompi/2021b gompi/2021a gompi/2020a |
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | |
| GOOGLETEST | googletest/1.15.2 googletest/1.14.0 googletest/1.13.0 googletest/1.12.1 googletest/1.11.0 |
Google's framework for writing C++ tests on a variety of platforms | |
| GOTRANSEQ | gotranseq/0.4.0 |
Translate nucleic acid sequences to their corresponding peptide sequences. | |
| GPAW | GPAW/23.9.1 |
GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. | |
| GPAW-SETUPS | GPAW-setups/0.9.20000 |
PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. | |
| GPERF | gperf/3.3 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. | |
| GPERFTOOLS | gperftools/2.13 gperftools/2.12 gperftools/2.10 |
gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. | |
| GRADLE | Gradle/8.6-Java-17 |
Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. | |
| GRAPHALIGNER | GraphAligner/1.0.20 GraphAligner/1.0.19 |
Seed-and-extend program for aligning long error-prone reads to genome graphs. | |
| GRAPHENE | Graphene/1.10.8 |
Graphene is a thin layer of types for graphic libraries | |
| GRAPHITE2 | graphite2/1.3.14 |
Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world. | |
| GRAPHVIZ | Graphviz/8.1.0 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. | |
| GRASS | GRASS/8.4.0 |
The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization | |
| GREAT_TABLES | great_tables/0.17.0 |
Make awesome display tables using Python. | |
| GROFF | groff/1.23.0 groff/1.22.4 |
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. | |
| GROMACS | GROMACS/2024.4-PLUMED-2.9.3 GROMACS/2024.4-PLUMED-2.9.2 GROMACS/2024.4-CUDA-12.4.1 GROMACS/2024.4-CUDA-12.4.0-PLUMED-2.9.3 GROMACS/2024.4-CUDA-12.4.0-PLUMED-2.9.2 GROMACS/2024.1 GROMACS/2024.1-CHAP GROMACS/2023.1 GROMACS/2021.5-CUDA-11.4.1-PLUMED-2.8.0 GROMACS/2021.5-CUDA-11.4.1-PLUMED-2.8.0-PyTorch-1.12.1 |
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 CPU only build, containing both MPI and threadMPI binaries for both single and double precision. It also contains the gmxapi extension for the single precision MPI build. | HPRC Docs |
| GRPC | gRPC/1.62.1 |
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. | |
| GRPCIO | grpcio/1.70.0 grpcio/1.62.1 grpcio/1.57.0 grpcio/1.56.2 grpcio/1.51.1 |
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. | |
| GST-PLUGINS-BAD | GST-plugins-bad/1.22.5 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/1.22.5 GST-plugins-base/1.22.1 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/1.22.5 GStreamer/1.22.1 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/2.4.1 GTDB-Tk/2.3.2 |
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. | |
| GTFTOGENEPRED | gtfToGenePred/482 |
Convert a GTF file to a genePred | |
| GTK2 | GTK2/2.24.33 |
The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. | |
| GTK3 | GTK3/3.24.42 GTK3/3.24.39 GTK3/3.24.37 GTK3/3.24.35 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 | GTK4/4.13.1 GTK4/4.11.3 |
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. | |
| GUILE | Guile/3.0.9 |
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/9.5.1 |
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. | |
| GZIP | gzip/1.13 gzip/1.12 gzip/1.10 |
gzip (GNU zip) is a popular data compression program as a replacement for compress | |
| H5PY | h5py/3.12.1 h5py/3.11.0 h5py/3.9.0 h5py/3.8.0 h5py/3.7.0 |
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. | |
| HAPHIC | HapHiC/2025.01.24 |
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data | |
| HARFBUZZ | HarfBuzz/11.2.1 HarfBuzz/9.0.0 HarfBuzz/8.2.2 HarfBuzz/5.3.1 HarfBuzz/4.2.1 HarfBuzz/2.8.1 |
HarfBuzz is an OpenType text shaping engine. | |
| HATCH-JUPYTER-BUILDER | hatch-jupyter-builder/0.9.1 |
Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets. | |
| HATCHLING | hatchling/1.27.0 hatchling/1.24.2 hatchling/1.18.0 |
Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager. | |
| HDF | HDF/4.3.0 HDF/4.2.16-2 HDF/4.2.16-2-w-fortran HDF/4.2.16-2-w-fortran-no-netCDF 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 | HDF5/1.14.5 HDF5/1.14.3 HDF5/1.14.0 HDF5/1.13.1 HDF5/1.12.2 HDF5/1.12.1 HDF5/1.10.7 |
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 |
HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelation of a sphere. It was designed to create a mathematical structure which supports a suitable discretization of functions on a sphere at sufficiently high resolution, and to facilitate fast and accurate statistical and astrophysical analysis of massive full-sky data sets. | |
| HELITRONSCANNER | HelitronScanner/1.1-Java-11 |
HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes | |
| HELP2MAN | help2man/1.49.3 help2man/1.49.2 help2man/1.48.3 help2man/1.47.16 help2man/1.47.12 help2man/1.47.8 help2man/1.47.4 |
help2man produces simple manual pages from the '--help' and '--version' output of other commands. | |
| HERRO | HERRO/20241210 HERRO/0.1.0_20240808 |
This is the github scripts for HERRO, which also load HERRO-env and HERRO-container. HERRO (Haplotype-aware ERRor cOrrection) is a highly accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1, Kit 14 reads (length of ≥ 10000bp is recommended). An experimental model for R9.4.1 data is also provided for download. | |
| HERRO-CONTAINER | HERRO-container/0.2.0 |
HERRO (Haplotype-aware ERRor cOrrection) is a highly accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1, Kit 14 reads (length of ≥ 10000bp is recommended). An experimental model for R9.4.1 data is also provided for download. | |
| HERRO-ENV | HERRO-env/20241210 |
This is the conda environment for HERRO. HERRO (Haplotype-aware ERRor cOrrection) is a highly accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1, Kit 14 reads (length of ≥ 10000bp is recommended). An experimental model for R9.4.1 data is also provided for download. | |
| HH-SUITE | HH-suite/3.3.0 |
The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). | |
| HICMATRIX | HiCMatrix/17 |
This library implements the central class of HiCExplorer to manage Hi-C interaction matrices. | |
| HIFIASM | hifiasm/0.25.0 hifiasm/0.24.0 hifiasm/0.23.0 hifiasm/0.21.0 hifiasm/0.19.7 |
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. | |
| HIFIASM-META | hifiasm-meta/0.3.2 |
A hifiasm fork for metagenome assembly using Hifi reads. | |
| HIGHWAY | Highway/1.0.4 Highway/1.0.3 |
Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'. | |
| HIREDIS | hiredis/1.2.0 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. | |
| 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/3.4 HMMER/3.4-ips5 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. | |
| HMMLEARN | hmmlearn/0.3.3 hmmlearn/0.3.0 hmmlearn/0.2.1 |
hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models | |
| HOMER | HOMER/4.11.1 |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. | |
| HPRC_UTILS | HPRC_utils/1.0 |
HPRC_utils is a collection of useful utilities to accompany software modules on the TAMU HPRC clusters. | |
| HTSLIB | HTSlib/1.21 HTSlib/1.19.1 HTSlib/1.18 HTSlib/1.17 HTSlib/1.15.1 |
A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix | |
| HUGGINGFACE_HUB | huggingface_hub/0.34.4 |
The huggingface_hub library allows you to interact with the Hugging Face Hub, a platform democratizing open-source Machine Learning for creators and collaborators. Discover pre-trained models and datasets for your projects or play with the thousands of machine learning apps hosted on the Hub. You can also create and share your own models, datasets and demos with the community. The huggingface_hub library provides a simple way to do all these things with Python. | |
| HWLOC | hwloc/2.11.2 hwloc/2.10.0 hwloc/2.9.2 hwloc/2.9.1 hwloc/2.8.0 hwloc/2.7.1 hwloc/2.5.0 hwloc/2.4.1 hwloc/2.2.0 |
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. | |
| HYPEROPT | Hyperopt/0.2.7 |
hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions. | |
| HYPHY | HyPhy/2.5.71 |
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 | |
| HYPOTHESIS | hypothesis/6.133.2 hypothesis/6.119.0 hypothesis/6.103.1 hypothesis/6.90.0 hypothesis/6.82.0 hypothesis/6.68.2 hypothesis/6.46.7 hypothesis/6.14.6 hypothesis/6.13.1 hypothesis/4.57.1 hypothesis/4.57.1-Python-2.7.18 |
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. | |
| HYPRE | Hypre/2.32.0 Hypre/2.31.0 Hypre/2.29.0 Hypre/2.28.0 Hypre/2.27.0 Hypre/2.25.0 |
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. | |
| ICU | ICU/76.1 ICU/75.1 ICU/74.1 ICU/73.2 ICU/72.1 ICU/71.1 ICU/69.1 |
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. | |
| IGPROF | IgProf/5.9.18 |
IgProf is a simple nice tool for measuring and analysing application memory and performance characteristics. | |
| IGV | IGV/2.19.1-Java-21 |
This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. | HPRC Docs |
| IIMPI | iimpi/2024a iimpi/2023b iimpi/2023a iimpi/2022b iimpi/2022a |
Intel C/C++ and Fortran compilers, alongside Intel MPI. | |
| IMAGEIO | imageio/2.34.1 imageio/2.33.1 imageio/2.31.1 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. | |
| IMAGEMAGICK | ImageMagick/7.1.1-38 ImageMagick/7.1.1-34 ImageMagick/7.1.1-15 ImageMagick/7.1.0-53 ImageMagick/7.1.0-37 |
ImageMagick is a software suite to create, edit, compose, or convert bitmap images | |
| IMATH | Imath/3.1.11 Imath/3.1.9 Imath/3.1.7 Imath/3.1.6 Imath/3.1.5 |
Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics | |
| IMBALANCED-LEARN | imbalanced-learn/0.10.1 |
imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance. | |
| IMKL | imkl/2024.2.0 imkl/2024.0.0 imkl/2023.2.0 imkl/2023.1.0 imkl/2022.2.1 imkl/2022.1.0 |
Intel oneAPI Math Kernel Library | |
| IMKL-FFTW | imkl-FFTW/2024.2.0 imkl-FFTW/2023.2.0 imkl-FFTW/2023.1.0 imkl-FFTW/2022.1.0 |
FFTW interfaces using Intel oneAPI Math Kernel Library | |
| IMOD | IMOD/5.1.5-CUDA-12.1.1 |
IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado. | |
| IMPI | impi/2021.13.0 impi/2021.10.0 impi/2021.9.0 impi/2021.7.1 impi/2021.6.0 |
Intel MPI Library, compatible with MPICH ABI | |
| INFERCNV | InferCNV/1.22.0-R-4.2.1 |
InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. | |
| INFERNAL | Infernal/1.1.5 Infernal/1.1.4 |
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. | |
| INTEL | intel/2024a intel/2023b intel/2023a intel/2022a |
Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). | |
| INTEL-COMPILERS | intel-compilers/2024.2.0 intel-compilers/2024.0.0 intel-compilers/2023.2.1 intel-compilers/2023.1.0 intel-compilers/2022.2.1 intel-compilers/2022.1.0 |
Intel C, C++ & Fortran compilers (classic and oneAPI) | |
| INTERPROSCAN | InterProScan/5.75-106.0 InterProScan/5.74-105.0 |
InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. | |
| 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. | |
| IPHOP | iphop/1.3.3 |
A bioinformatic tool for computational prediction of host taxonomy from phage genomes. | |
| IPYMPL | ipympl/0.9.3 |
Leveraging the Jupyter interactive widgets framework, ipympl enables the interactive features of matplotlib in the Jupyter notebook and in JupyterLab. Besides, the figure canvas element is a proper Jupyter interactive widget which can be positioned in interactive widget layouts. | |
| IQ-TREE | IQ-TREE/2.3.6 IQ-TREE/2.3.5 IQ-TREE/2.2.2.3 IQ-TREE/1.6.12 |
Efficient phylogenomic software by maximum likelihood | |
| IRF | IRF/3.09 |
Inverted Repeats Finder (IRF) | |
| ISA-L | ISA-L/2.31.0 ISA-L/2.30.0 |
Intelligent Storage Acceleration Library | |
| ISL | ISL/0.26 ISL/0.24 |
isl is a library for manipulating sets and relations of integer points bounded by linear constraints. | |
| ISONET | IsoNet/0.3-CUDA-12.1.1 |
Isotropic Reconstruction of Electron Tomograms with Deep Learning | |
| ISOSEQ | IsoSeq/4.3.0-linux-x86_64 |
IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added. | |
| ITK | ITK/5.3.0 |
Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. | |
| JAGS | JAGS/4.3.1 |
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/4.2.5 JasPer/4.2.4 JasPer/4.0.0 JasPer/2.0.33 JasPer/2.0.28 |
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/21.0.2 Java/17.0.6 Java/17.0.4 Java/11.0.27 Java/11.0.20 Java/11.0.2 Java/1.8.0_292-OpenJDK |
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. | |
| 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. | |
| JBROWSE | JBrowse/1.16.12 |
JBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. | HPRC Docs |
| JEDI | jedi/0.19.1 jedi/0.19.0 |
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/5.3.0 jemalloc/5.2.1 |
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. | |
| JOYPY | joypy/0.2.6 |
Joyplots in Python with matplotlib & pandas | |
| JQ | jq/1.6 |
jq is a lightweight and flexible command-line JSON processor. | |
| JSON-C | json-c/0.17 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. | |
| JSON-FORTRAN | json-fortran/9.0.3 json-fortran/9.0.2 |
JSON-Fortran: A Modern Fortran JSON API | |
| JSONCPP | 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. | |
| JUICER | Juicer/1.6-Java-11-CUDA-11.7.0-CPU |
Juicer is a one-click pipeline for processing terabase scale Hi-C datasets. | |
| JUICER_TOOLS | Juicer_tools/1.22.01-Java-11-CUDA-11.7.0 |
Tools for use with the Juicer application. | |
| JULIA | Julia/1.11.3-linux-x86_64 |
Julia is a high-level, high-performance dynamic programming language for numerical computing | HPRC Docs |
| JUPYTER-BUNDLE | Jupyter-bundle/20230823 |
This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub. | |
| JUPYTER-RESOURCE-USAGE | jupyter-resource-usage/1.0.0 |
Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU) | |
| JUPYTER-SERVER | jupyter-server/2.14.0 jupyter-server/2.7.2 jupyter-server/2.7.0 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. | |
| JUPYTER-SERVER-PROXY | jupyter-server-proxy/4.0.0 jupyter-server-proxy/3.2.2 |
Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example. | |
| JUPYTERLMOD | jupyterlmod/5.2.1 jupyterlmod/4.0.3 |
Jupyter interactive notebook server extension that allows users to interact with environment modules before launching kernels. The extension uses Lmod's Python interface to accomplish module-related tasks like loading, unloading, saving collections, etc. | |
| JUPYTERNOTEBOOK | JupyterNotebook/7.2.0 JupyterNotebook/7.0.3 JupyterNotebook/7.0.2 |
The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience. | |
| K8 | k8/1.2 |
A JavaScript runtime built on top of the Google V8 JavaScript engine. | |
| KAHIP | KaHIP/3.16 KaHIP/3.14 |
The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. | |
| KAIJU | Kaiju/1.10.1 |
Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments | |
| KAKS_CALCULATOR | KaKs_Calculator/2.0.1 |
KaKs_Calculator is capable for calculating selective pressure on both coding and non-coding sequences. | |
| KALEIDO | Kaleido/0.2.1 |
Fast static image export for web-based visualization libraries with zero dependencies | |
| KALIGN | Kalign/3.4.0 Kalign/3.3.5 |
Kalign is a fast multiple sequence alignment program for biological sequences. | |
| KALLISTO | kallisto/0.51.1 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. | |
| KENT_TOOLS | Kent_tools/20241218-linux.x86_64 Kent_tools/468 Kent_tools/442 |
Kent tools: collection of tools used by the UCSC genome browser. | |
| 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. | |
| KINETICSTOOLS | kineticsTools/0.8.0 |
Tools for detecting DNA modifications from single molecule, real-time (SMRT®) sequencing data. This tool implements the P_ModificationDetection module in SMRT® Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol. Researchers interested in understanding or extending the modification detection algorthims can use these tools as a starting point. | |
| KINETO | kineto/0.4.0 |
A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters | |
| KMA | kma/1.6.6 |
KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. | |
| KNEADDATA | kneaddata/0.12.2 |
KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments. | |
| KOFAMSCAN | KofamScan/1.0 |
KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. | |
| 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 | Kraken2/2.1.6 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. | |
| KRBALANCING | krbalancing/0.5.0b0 |
A C++ extension for Python which computes K.R. balanced matrices. | |
| 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. | |
| LAME | LAME/3.100 |
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. | |
| LAMMPS | LAMMPS/29Aug2024-kokkos LAMMPS/28Oct2024-kokkos-mace-CUDA-12.1.1-CC-86 LAMMPS/28Oct2024-kokkos-mace-CUDA-12.1.1-CC-80 LAMMPS/28Oct2024-kokkos-mace-CUDA-12.1.1-CC-75 LAMMPS/28Oct2024-gpu-package-CUDA-12.1.1-CC-86 LAMMPS/28Oct2024-gpu-package-CUDA-12.1.1-CC-80 LAMMPS/28Oct2024-gpu-package-CUDA-12.1.1-CC-75 LAMMPS/2Aug2023_update2-kokkos LAMMPS/2Aug2023_update2-kokkos-CUDA-12.1.1-CC-86 LAMMPS/2Aug2023_update2-kokkos-CUDA-12.1.1-CC-80 LAMMPS/2Aug2023_update2-kokkos-CUDA-12.1.1-CC-75 LAMMPS/2Aug2023_update2-gpu-package-CUDA-12.1.1-CC-86 LAMMPS/2Aug2023_update2-gpu-package-CUDA-12.1.1-CC-80 LAMMPS/2Aug2023_update2-gpu-package-CUDA-12.1.1-CC-75 |
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. | HPRC Docs |
| LAPACK | LAPACK/3.12.0 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. | |
| LAST | LAST/1045 |
LAST finds similar regions between sequences. | |
| LDC | LDC/1.36.0 LDC/1.24.0-x86_64 |
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). | |
| LEVMAR | levmar/2.6 |
This is levmar, a copylefted C/C++ implementation of the Levenberg-Marquardt non-linear least squares algorithm. levmar includes double and single precision LM versions, both with analytic and finite difference approximated Jacobians. levmar also has some support for constrained non-linear least squares, allowing linear equation, box and linear inequality constraints. | |
| LFTP | lftp/4.9.3 |
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. | |
| LHAPDF | LHAPDF/6.5.5 |
LHAPDF is the standard tool for evaluating parton distribution functions (PDFs) in high-energy physics. PDFs encode the flavour and momentum structure of composite particles, such as protons, pions and nuclei; most cross-section calculations are based on parton-level matrix-elements which must be connected to the real interacting particles, hence PDFs are an essential ingredient of phenomenological and experimental studies at hadron and heavy-ion colliders (e.g. LHC, HERA, Tevatron, EIC, FCC) and in cosmic-ray physics. | |
| LIBAEC | libaec/1.1.3 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/0.3.113 libaio/0.3.112 |
Asynchronous input/output library that uses the kernels native interface. | |
| LIBARCHIVE | libarchive/3.7.7 libarchive/3.7.4 libarchive/3.7.2 libarchive/3.6.2 libarchive/3.6.1 libarchive/3.5.1 libarchive/3.4.3 |
Multi-format archive and compression library | |
| LIBATOMIC_OPS | libatomic_ops/7.8.2 |
This package provides semi-portable access to hardware-provided atomic memory update operations on a number of architectures. | |
| LIBAVIF | libavif/1.0.4 |
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/2.4 libcerf/2.3 libcerf/2.1 libcerf/1.17 |
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. | |
| LIBCIRCLE | libcircle/0.3 |
An API to provide an efficient distributed queue on a cluster. libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization. | |
| LIBDAP | libdap/3.21.0-131 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. | |
| LIBDE265 | libde265/1.0.16 libde265/1.0.15 libde265/1.0.11 |
libde265 is an open source implementation of the h.265 video codec | |
| LIBDEFLATE | libdeflate/1.24 libdeflate/1.20 libdeflate/1.19 libdeflate/1.18 libdeflate/1.15 libdeflate/1.10 |
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. | |
| LIBDIVSUFSORT | libdivsufsort/2.0.1 |
libdivsufsort is a software library that implements a lightweight suffix array construction algorithm. | |
| LIBDRM | libdrm/2.4.125 libdrm/2.4.122 libdrm/2.4.117 libdrm/2.4.115 libdrm/2.4.114 libdrm/2.4.110 libdrm/2.4.106 |
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 libevent/2.1.11 |
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. | |
| LIBFABRIC | libfabric/2.0.0 libfabric/1.21.0 libfabric/1.19.0 libfabric/1.18.0 libfabric/1.16.1 libfabric/1.15.1 libfabric/1.13.2 libfabric/1.12.1 libfabric/1.11.0 |
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. | |
| LIBFDF | libfdf/0.5.1 |
LibFDF is the official implementation of the FDF specifications for use in client codes. | |
| LIBFFI | libffi/3.4.5 libffi/3.4.4 libffi/3.4.2 libffi/3.3 |
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/1.10.3 |
Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG | |
| LIBGD | libgd/2.3.3 libgd/2.3.1 |
GD is an open source code library for the dynamic creation of images by programmers. | |
| LIBGEOTIFF | libgeotiff/1.7.3 libgeotiff/1.7.1 libgeotiff/1.6.0 |
Library for reading and writing coordinate system information from/to GeoTIFF files | |
| LIBGIT2 | libgit2/1.8.1 libgit2/1.7.2 libgit2/1.7.1 libgit2/1.5.0 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. | |
| LIBGLU | libGLU/9.0.3 libGLU/9.0.2 libGLU/9.0.1 |
The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. | |
| LIBGLVND | libglvnd/1.7.0 libglvnd/1.6.0 libglvnd/1.4.0 libglvnd/1.3.3 |
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. | |
| LIBGPG-ERROR | libgpg-error/1.48 |
Libgpg-error is a small library that defines common error values for all GnuPG components. | |
| LIBGRIDXC | libGridXC/2.0.2 |
A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems. | |
| LIBHARU | libharu/2.4.4 libharu/2.3.0 |
libHaru is a free, cross platform, open source library for generating PDF files. | |
| LIBHEIF | libheif/1.19.8 libheif/1.19.5 libheif/1.17.6 libheif/1.16.2 |
libheif is an HEIF and AVIF file format decoder and encoder | |
| LIBICONV | libiconv/1.18 libiconv/1.17 libiconv/1.16 |
Libiconv converts from one character encoding to another through Unicode conversion | |
| LIBIDN2 | libidn2/2.3.8 libidn2/2.3.7 libidn2/2.3.4 libidn2/2.3.2 |
Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. | |
| 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. | |
| LIBJPEG-TURBO | libjpeg-turbo/3.1.0 libjpeg-turbo/3.0.1 libjpeg-turbo/2.1.5.1 libjpeg-turbo/2.1.4 libjpeg-turbo/2.1.3 libjpeg-turbo/2.0.6 |
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. | |
| LIBLEIDENALG | libleidenalg/0.11.1 |
Implements the Leiden algorithm in C++ | |
| LIBMAD | libmad/0.15.1b |
MAD is a high-quality MPEG audio decoder. | |
| LIBNSL | libnsl/2.0.1 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/1.5.2 libopus/1.4 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/0.18.1 libpciaccess/0.17 libpciaccess/0.16 |
Generic PCI access library. | |
| LIBPNG | libpng/1.6.48 libpng/1.6.43 libpng/1.6.40 libpng/1.6.39 libpng/1.6.38 libpng/1.6.37 |
libpng is the official PNG reference library | |
| LIBPSL | libpsl/0.21.5 |
C library for the Public Suffix List | |
| LIBPSML | libPSML/2.1.0 |
A library to handle pseudopotentials in PSML format | |
| LIBREADLINE | libreadline/8.2 libreadline/8.1.2 libreadline/8.1 libreadline/8.0 |
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. | |
| 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. | |
| LIBROSA | librosa/0.10.1 |
Audio and music processing in Python | |
| 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++/3.6.0 libsigc++/3.4.0 |
The libsigc++ package implements a typesafe callback system for standard C++. | |
| LIBSNDFILE | libsndfile/1.2.2 libsndfile/1.2.0 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/1.0.19 libsodium/1.0.18 |
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. | |
| LIBSOUP | LibSoup/3.6.1 |
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. | |
| LIBSPATIALITE | libspatialite/5.1.0 |
SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. | |
| 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. | |
| 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. | |
| LIBTIFF | LibTIFF/4.7.0 LibTIFF/4.6.0 LibTIFF/4.5.0 LibTIFF/4.4.0 LibTIFF/4.3.0 LibTIFF/4.2.0 |
tiff: Library and tools for reading and writing TIFF data files | |
| LIBTIRPC | libtirpc/1.3.5 libtirpc/1.3.4 libtirpc/1.3.3 libtirpc/1.3.2 |
Libtirpc is a port of Suns Transport-Independent RPC library to Linux. | |
| LIBTOOL | libtool/2.5.4 libtool/2.4.7 libtool/2.4.6 |
GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. | |
| LIBUNISTRING | libunistring/1.3 libunistring/1.1 |
This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. | |
| LIBUNWIND | libunwind/1.8.1 libunwind/1.6.2 libunwind/1.4.0 |
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 | |
| LIBURING | liburing/2.9 |
Library providing helpers for the Linux kernel io_uring support. | |
| LIBVDWXC | libvdwxc/0.4.0 |
libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes. | |
| 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/1.5.0 libwebp/1.4.0 libwebp/1.3.2 libwebp/1.3.1 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/1.16.0 |
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/6.2.2 libxc/5.2.3 |
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. | |
| 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. | |
| LIBXML2 | libxml2/2.13.4 libxml2/2.12.7 libxml2/2.11.5 libxml2/2.11.4 libxml2/2.10.3 libxml2/2.9.13 libxml2/2.9.10 |
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). | |
| LIBXSLT | libxslt/1.1.42 libxslt/1.1.38 libxslt/1.1.37 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. | |
| LIFTOFF | Liftoff/1.6.3 |
Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species. | |
| LINKS | LINKS/1.8.7 |
LINKS is a genomics application for scaffolding or re-scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It provides a generic framework for scaffolding and can work on any sequences. | |
| LIT | lit/18.1.8 lit/18.1.7 lit/18.1.2 |
lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures. | |
| LITTLECMS | LittleCMS/2.17 LittleCMS/2.16 LittleCMS/2.15 LittleCMS/2.14 LittleCMS/2.13.1 |
Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. | |
| LLVM | LLVM/20.1.7 LLVM/18.1.8 LLVM/18.1.8-minimal LLVM/16.0.6 LLVM/15.0.5 LLVM/14.0.6 LLVM/14.0.6-llvmlite LLVM/14.0.3 LLVM/11.1.0 |
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. | |
| LMFIT | LMfit/1.2.2 |
Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python | |
| LMOD | lmod/ |
Lmod: An Environment Module System | |
| LOG4CPP | log4cpp/1.1.4 |
Log4cpp is library of C++ classes for flexible logging to files, syslog, IDSA and other destinations. | |
| 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. | |
| LONGQC | LongQC/1.2.0 |
LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc. | |
| LONGRANGER | longranger/2.2.2 |
Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. | |
| LONGSTITCH | LongStitch/1.0.5 |
A genome assembly correction and scaffolding pipeline using long reads | |
| LRSLIB | lrslib/7.2 |
lrslib is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems | |
| LS-DYNA | LS-DYNA/R15.0.2 LS-DYNA/R14.1.0 |
LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. - Homepage: http://www.lstc.com/products/ls-dyna/ | |
| LS-OPT | LS-OPT/2025R1 |
LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA. - Homepage: http://www.lstc.com/products/ls-opt/ | |
| LS-PREPOST | LS-PREPOST/4.12 LS-PREPOST/4.12-dpLS-PrePost/4.7.15 |
LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. | |
| LSD2 | LSD2/2.4.1 LSD2/2.3 |
Least-squares methods to estimate rates and dates from phylogenies | |
| LTR_RETRIEVER | LTR_retriever/3.0.1 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. | |
| LUA | Lua/5.4.7 Lua/5.4.6 Lua/5.4.4 Lua/5.4.3 |
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. | |
| LWGRP | lwgrp/1.0.6 |
The light-weight group library defines data structures and collective operations to group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators when the overhead of communicator creation is too costly. For example, certain sorting algorithms recursively divide processes into subgroups as the sort algorithm progresses. These groups may be different with each invocation, so that it is inefficient to create and destroy communicators during the sort routine. | |
| LXML | lxml/5.3.0 lxml/4.9.3 lxml/4.9.2 lxml/4.9.1 |
The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. | |
| LZO | LZO/2.10 |
Portable lossless data compression library | |
| M4 | M4/1.4.20 M4/1.4.19 M4/1.4.18 M4/1.4.17 |
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 | MACS2/2.2.9.1 |
Model Based Analysis for ChIP-Seq data | |
| MAEPARSER | maeparser/1.3.0 |
maeparser is a parser for Schrodinger Maestro files. | |
| MAFFT | MAFFT/7.526-with-extensions MAFFT/7.520-with-extensions 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. | |
| MAGMA | magma/2.7.2-CUDA-12.1.1 magma/2.6.2-CUDA-11.7.0 magma/2.6.2-CUDA-11.4.1 |
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/4.4.1 make/4.3 |
GNU version of make utility | |
| MAKEDEPEND | makedepend/1.0.7 makedepend/1.0.6 |
The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. | |
| MAKEINFO | makeinfo/7.1 makeinfo/7.0.3 makeinfo/6.8 makeinfo/6.7 |
makeinfo is part of the Texinfo project, the official documentation format of the GNU project. | |
| MAKER | MAKER/3.01.03 |
A portable and easily configurable genome annotation pipeline. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. | |
| MAKO | Mako/1.3.10 Mako/1.3.5 Mako/1.2.4 Mako/1.2.0 Mako/1.1.4 |
A super-fast templating language that borrows the best ideas from the existing templating languages | |
| MAMBA | Mamba/23.11.0-0 |
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. | |
| MAPCLASSIFY | mapclassify/2.8.1 |
Implements a family of classification schemes for choropleth maps. | |
| MARIADB | MariaDB/11.7.0 MariaDB/11.6.0 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 | |
| MASHMAP | MashMap/3.1.3 |
A fast approximate aligner for long DNA sequences. | |
| MATHEMATICA | Mathematica/13.2 |
Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. | |
| MATPLOTLIB | matplotlib/3.10.3 matplotlib/3.9.2 matplotlib/3.8.2 matplotlib/3.7.2 matplotlib/3.7.0 matplotlib/3.5.2 |
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. | |
| MATURIN | maturin/1.8.3 maturin/1.8.3-Rust-1.83.0 maturin/1.6.0 maturin/1.5.0-Rust-1.76.0 maturin/1.4.0-Rust-1.75.0 maturin/1.3.1 maturin/1.1.0 |
This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support. | |
| MAVEN | Maven/3.9.7 |
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. | |
| MAXQUANT | MaxQuant/2.7.0.0 |
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. | |
| MCL | MCL/22.282 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. | |
| MCSCANX | MCScanX/2024.19.19 MCScanX/2024.12.19 MCScanX/1.0.0 |
MCScanX, implementing a modified MCScan algorithm, detects syntenic blocks and progressively aligns multiple syntenic blocks against reference genomes (PIVOT). | |
| MCTC-LIB | mctc-lib/0.3.1 |
Common tool chain for working with molecular structure data in various applications. This library provides a unified way to perform operations on molecular structure data, like reading and writing to common geometry file formats. | |
| MDI | MDI/1.4.29 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. | |
| MEDAKA | medaka/1.12.0 |
medaka is a tool to create a consensus sequence from nanopore sequencing data. | |
| MEGAHIT | MEGAHIT/1.2.9 |
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph | |
| MEMXTERMINATOR | MemXTerminator/1.2.2-CUDA-11.7.0 |
A software for membrane analysis and subtraction in cryo-EM. | |
| MERCURIAL | Mercurial/6.4.5 |
Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. | |
| MERQURY | Merqury/1.3 |
Evaluate genome assemblies with k-mers and more Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose. | |
| MERYL | Meryl/1.4.1 |
This is Meryl, a near total rewrite of 'meryl' that appeared in both project kmer and Celera Assembler. This is not compatible with old meryl dbs built from canu 1.8 or earlier. The new Meryl is significantly faster than the previous version. Meryl dbs are no longer in .mcdat and .mcidx file format. Meryl db is now designed as a DIRECTORY, containing 64 binaries + 64 indexes (128 files). | |
| MESA | Mesa/25.1.3 Mesa/24.1.3 Mesa/23.1.9 Mesa/23.1.4 Mesa/22.2.4 Mesa/22.0.3 Mesa/21.1.1 |
Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. | |
| MESON-PYTHON | meson-python/0.18.0 meson-python/0.16.0 meson-python/0.15.0 meson-python/0.13.2 |
Python build backend (PEP 517) for Meson projects | |
| METABAT | MetaBAT/2.17 |
An efficient tool for accurately reconstructing single genomes from complex microbial communities | |
| METABOLIC | METABOLIC/2024.01.18 |
METabolic And BiogeOchemistry anaLyses In miCrobes | |
| METACERBERUS | MetaCerberus/1.4.0 |
MetaCerberus transforms raw sequencing (i.e. genomic, transcriptomics, metagenomics, metatranscriptomic) data into knowledge. | |
| METADECODER | MetaDecoder/1.0.19 |
An algorithm for clustering metagenomic sequences | |
| METAEUK | MetaEuk/6 |
MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. | |
| METAMDBG | metaMDBG/1.2 |
MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). It is based on the minimizer de-Bruijn graph (MDBG), which have been reimplemented specifically for metagenomics assembly. MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity. | |
| METAPHLAN | MetaPhlAn/4.2.4 MetaPhlAn/4.2.2 MetaPhlAn/4.1.0 MetaPhlAn/4.0.6 |
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling. | |
| 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. | |
| MGSE | MGSE/3.1 |
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly. | |
| MICRO-C | Micro-C/2023.08.01 |
Micro-C QC and data analysis | |
| MICROMAMBA | micromamba/2.3.3-0 micromamba/2.1.0-0 |
A statically-linked single file version of Mamba. | |
| MINICONDA3 | Miniconda3/24.11.1 Miniconda3/23.10.0-1 Miniconda3/23.9.0-0 Miniconda3/23.5.2-0 Miniconda3/4.12.0 Miniconda3/4.9.2 |
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 | Miniforge3/25.3.0-3 Miniforge3/24.11.3-0 |
Miniforge is a free minimal installer for conda and Mamba specific to conda-forge. | |
| MINIMAP2 | minimap2/2.29 minimap2/2.28 minimap2/2.26 minimap2/2.24 minimap2/2.17 |
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. | |
| MINIPROT | miniprot/0.13 |
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much faster at the residue alignment step. | |
| MINIZIP | minizip/1.1 |
Mini zip and unzip based on zlib | |
| MINPATH | MinPath/1.6 |
MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. | |
| MIRNA | miRNA/0.2.8 |
The BCGSC miRNA Profiling Pipeline produces expression profiles of known miRNAs from BWA-aligned BAM files and generates summary reports and graphs describing the results. | |
| MITOGRAPH | MitoGraph/3.1 |
MitoGraph is a fully automated image processing method and software dedicated to calculating the three-dimensional morphology of mitochondria in live cells. | |
| MITOHIFI | MitoHiFi/3.2 |
MitoHiFi is a Python workflow that assembles mitogenomes from Pacbio HiFi reads | |
| MITOZ | MitoZ/3.6 |
MitoZ provides a "one-click" solution to get annotated mitogenomes from raw data fastq files. | |
| ML-COLLECTIONS | ml-collections/0.1.1 |
ML Collections is a library of Python Collections designed for ML use cases. | |
| MLST | mlst/2.23.0 |
Scan contig files against traditional PubMLST typing schemes | |
| ML_DTYPES | ml_dtypes/0.5.0 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/1.0.6 mm-common/1.0.5 |
The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries. | |
| MM2-PLUS | mm2-plus/1.0 |
mm2-plus is an fast long-read to genome and genome-to-genome aligner, built on top of minimap2 (Minimap2-2.28 (r1209)). | |
| MMG | Mmg/5.8.0 |
Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries. | |
| MMSEQS2 | MMseqs2/14-7e284 |
MMseqs2: ultra fast and sensitive search and clustering suite | |
| MODELTEST-NG | ModelTest-NG/0.1.7-Linux64 |
ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces. | |
| MODKIT | Modkit/0.4.4modkit/0.4.4 |
A bioinformatics tool for working with modified bases. | |
| MOLDEN | Molden/7.3 |
Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac | |
| MOPAC | MOPAC/23.1.2 |
MOPAC is a general-purpose semiempirical molecular orbital package for the study of solid state and molecular structures and reactions. | |
| MOSDEPTH | mosdepth/0.3.11 |
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing | |
| MOTHUR | mothur/1.48.2 |
This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. | |
| 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. | |
| MPC | MPC/1.3.1 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/4.2.1 MPFR/4.2.0 MPFR/4.1.0 |
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. | |
| MPI4PY | mpi4py/4.0.1 mpi4py/3.1.6 mpi4py/3.1.5 mpi4py/3.1.4 mpi4py/3.1.1 mpi4py/3.0.3 |
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. | |
| MPICH | MPICH/4.2.2 |
MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). | |
| MPIFILEUTILS | mpifileutils/0.12 mpifileutils/0.11.1 |
MPI-Based File Utilities For Distributed Systems | |
| MRBAYES | MrBayes/3.2.7 |
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | |
| MRCFILE | mrcfile/1.5.0 |
mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. | |
| MSMC2 | msmc2/2.1.4 |
This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data. | |
| MSTORE | mstore/0.3.0 |
Molecular structure store for testing | |
| MUJOCO | MuJoCo/3.1.4 |
MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures interacting with their environment. | |
| MULTICHOOSE | multichoose/1.0.3 |
generate multiset combinations (n multichoose k). | |
| MULTIPROCESS | multiprocess/0.70.17 multiprocess/0.70.16-poetry multiprocess/0.70.15 |
better multiprocessing and multithreading in python | |
| MULTIQC | MultiQC/1.27.1 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. | |
| MULTIWFN | Multiwfn/3.8-dev |
Multiwfn is a very powerful program for realizing electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods. | |
| 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. | |
| MUMPS | MUMPS/5.7.2-metis MUMPS/5.6.1-metis MUMPS/5.5.1-metis |
A parallel sparse direct solver | |
| 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. | |
| NAMD | NAMD/3.0.1-muliticore-CUDA NAMD/3.0-mpi NAMD/2.14-mpi NAMD/2.14-CUDA-11.7.0 |
A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | HPRC Docs |
| NANOCOMP | NanoComp/1.24.0 |
Comparing runs of Oxford Nanopore sequencing data and alignments | |
| NANOGET | nanoget/1.19.3 |
Functions to extract information from Oxford Nanopore sequencing data and alignments | |
| NANOMATH | nanomath/1.4.0 |
A few simple math functions for other Oxford Nanopore processing scripts | |
| NANOPLOT | NanoPlot/1.43.0 |
Plotting suite for long read sequencing data and alignments | |
| NASM | NASM/2.16.03 NASM/2.16.01 NASM/2.15.05 |
NASM: General-purpose x86 assembler | |
| NAUTY | nauty/2.8.8 |
nauty and Traces are programs for computing automorphism groups of graphs and digraphs. They can also produce a canonical label. | |
| NBCLASSIC | nbclassic/1.0.0 |
NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking. | |
| NCBI-VDB | ncbi-vdb/3.2.0 ncbi-vdb/3.1.1 ncbi-vdb/3.0.10 ncbi-vdb/3.0.2 |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | |
| NCCL | NCCL/2.22.3-CUDA-12.6.0 NCCL/2.20.5-CUDA-12.4.1 NCCL/2.18.3-CUDA-12.1.1 NCCL/2.12.12-CUDA-11.7.0 NCCL/2.10.3-CUDA-11.4.1 |
The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. | |
| NCDU | ncdu/1.18 |
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. | |
| NCL | NCL/6.6.2 |
NCL is an interpreted language designed specifically for scientific data analysis and visualization. | HPRC Docs |
| NCO | NCO/5.2.9 NCO/5.1.0 |
The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. | |
| NCURSES | ncurses/6.5 ncurses/6.4 ncurses/6.3 ncurses/6.2 ncurses/6.1 |
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/2.1.11 |
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. | |
| NEDIT | NEdit/5.7.7 |
A fast, compact Motif/X11 plain text editor, for most popular Unix systems. | |
| NEPER | Neper/4.6.1neper/4.10.1 |
Neper is a free / open source software package for polycrystal generation and meshing. It can be used to generate polycrystals with a wide variety of morphological properties, from very simple morphologies (simple tessellations, grain-growth microstructures, …) to complex, multiphase or multiscale microstructures that involve grain subdivisions. The resulting tessellations can be meshed into high-quality meshes suitable for finite-element simulations. | |
| NETCDF | netCDF/4.9.2 netCDF/4.9.0 netCDF/4.8.1 netCDF/4.8.0 |
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. | HPRC Docs |
| 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-COMBINED | netCDF-combined/4.9.3-gompi-2023a netCDF-combined/4.9.3-gompi-2022a |
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/4.6.1 netCDF-Fortran/4.6.0 netCDF-Fortran/4.5.3 |
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/3.10 nettle/3.9.1 nettle/3.8.1 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/3.4.2 networkx/3.2.1 networkx/3.1 networkx/3.0 networkx/2.8.8 networkx/2.8.4 networkx/2.6.3 |
NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | |
| NEXTFLOW | Nextflow/25.04.6 Nextflow/24.10.3 Nextflow/23.10.0 |
Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data | |
| NGHTTP2 | nghttp2/1.58.0 |
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 | nghttp3/1.3.0 |
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. | |
| NGS | NGS/3.0.1-Java-11 |
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. | |
| NGSADMIX | NGSadmix/32 |
NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods. | |
| NGTCP2 | ngtcp2/1.2.0 |
Call it TCP/2. One More Time.' ngtcp2 project is an effort to implement RFC9000 QUIC protocol. | |
| NIM | Nim/2.2.0 |
Nim is a systems and applications programming language. | |
| NLOHMANN_JSON | nlohmann_json/3.11.3 nlohmann_json/3.11.2 nlohmann_json/3.10.5 |
JSON for Modern C++ | |
| 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. | |
| NLTK | NLTK/3.8.1 |
NLTK is a leading platform for building Python programs to work with human language data. | |
| NODEJS | nodejs/22.16.0 nodejs/20.13.1 nodejs/20.9.0 nodejs/18.17.1 nodejs/18.12.1 nodejs/16.15.1 |
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. | |
| NORMALIZ | Normaliz/3.10.3 |
Normaliz is a open source tool for computations in affine monoids, vector configurations, rational polyhedra and rational cones. Normaliz now computes rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic extensions of QQ. | |
| NOSE3 | nose3/1.3.8 |
Nose extends unittest to make testing easier. | |
| NSPR | NSPR/4.36 NSPR/4.35 NSPR/4.34 NSPR/4.30 |
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. | |
| NSS | NSS/3.113 NSS/3.104 NSS/3.94 NSS/3.89.1 NSS/3.85 NSS/3.79 NSS/3.65 |
Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. | |
| NSYNC | nsync/1.29.2 nsync/1.26.0 nsync/1.25.0 |
nsync is a C library that exports various synchronization primitives, such as mutexes | |
| NTL | NTL/11.5.1 |
NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields. | |
| NTLINK | ntLink/1.3.11 |
Minimizer-based genome assembly scaffolding and mapping using long reads and minimizers | |
| NTSYNT-VIZ | ntSynt-viz/1.0.0 |
ntSynt-viz: Visualizing multi-genome synteny | |
| NUMACTL | numactl/2.0.19 numactl/2.0.18 numactl/2.0.16 numactl/2.0.14 numactl/2.0.13 |
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/0.62.0 numba/0.61.2 numba/0.60.0 numba/0.58.1 numba/0.56.4 numba/0.56.4-CUDA-12.2.0 numba/0.56.4-CUDA-11.7.0 |
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. | |
| NVHPC | NVHPC/24.9-CUDA-12.6.0 NVHPC/24.9-CUDA-12.6.0-cc8.0 NVHPC/22.7-CUDA-11.7.0 NVHPC/21.9 |
C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) | |
| NWCHEM | NWChem/7.2.3 NWChem/7.2.2 |
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. | HPRC Docs |
| ODGI | ODGI/0.9.2-CUDA-12.6.0 |
Provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. | |
| ONNX | ONNX/1.17.0 |
Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types. Currently we focus on the capabilities needed for inferencing (scoring). | |
| ONT-FAST5-API | ont-fast5-api/4.1.2 ont-fast5-api/4.1.1 |
ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. | |
| 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. | |
| OPENBLAS | OpenBLAS/0.3.29 OpenBLAS/0.3.27 OpenBLAS/0.3.24 OpenBLAS/0.3.23 OpenBLAS/0.3.21 OpenBLAS/0.3.20 OpenBLAS/0.3.18 OpenBLAS/0.3.15 OpenBLAS/0.3.9 |
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | |
| OPENCV | OpenCV/4.8.1-CUDA-12.1.1-contrib OpenCV/4.8.0-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/3.2.4 OpenEXR/3.2.0 OpenEXR/3.1.7 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/11 OpenFOAM/10 OpenFOAM/9 OpenFOAM/8 OpenFOAM/7-20200508 OpenFOAM/6-20190620 OpenFOAM/6 OpenFOAM/v2406 OpenFOAM/v2206 OpenFOAM/v2106 |
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. | HPRC Docs |
| OPENGL | OpenGL/NVIDIA |
Originally developed by Silicon Graphics in the early '90s, OpenGL® has become the most widely-used open graphics standard in the world. NVIDIA supports OpenGL and a complete set of OpenGL extensions, designed to give you maximum performance on our GPUs. | |
| OPENJPEG | OpenJPEG/2.5.3 OpenJPEG/2.5.2 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/8.3.1-CUDA-12.2.0 OpenMM/8.2.0-CUDA-12.2.0 OpenMM/8.1.2 OpenMM/8.1.2-CUDA-12.2.0 OpenMM/8.1.1-CUDA-11.8.0 OpenMM/8.0.0-CUDA-12.1.1 OpenMM/8.0.0-CUDA-11.7.0 OpenMM/7.7.0-CUDA-11.7.0 OpenMM/7.5.0-CUDA-11.7.0 |
OpenMM is a toolkit for molecular simulation. | |
| OPENMPI | OpenMPI/5.0.7 OpenMPI/5.0.3 OpenMPI/4.1.8 OpenMPI/4.1.6 OpenMPI/4.1.5 OpenMPI/4.1.4 OpenMPI/4.1.1 OpenMPI/4.0.3 |
The Open MPI Project is an open source MPI-3 implementation. | |
| 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. | |
| OPENPYXL | openpyxl/3.1.5 openpyxl/3.1.2 |
A Python library to read/write Excel 2010 xlsx/xlsm files | |
| 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). | |
| OPENSLIDE-PYTHON | openslide-python/1.2.0 |
OpenSlide Python is a Python interface to the OpenSlide library. | |
| OPERA-MS | OPERA-MS/0.9.0-20240703 OPERA-MS/0.8.2 |
OPERA-MS is a hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies. | |
| OPTIX | OptiX/6.5.0 |
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. | |
| OPTREE | optree/0.14.1 |
Optimized PyTree Utilities | |
| ORCA | ORCA/6.1.1-avx2 ORCA/6.1.0-avx2 ORCA/6.0.1-avx2 ORCA/5.0.4 |
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. | |
| ORFM | OrfM/0.7.1 |
A simple and not slow open reading frame (ORF) caller. | |
| ORTHOFINDER | OrthoFinder/3.0.1b1 OrthoFinder/2.5.5 |
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics | |
| ORTHOGRAPH | Orthograph/0.7.1 |
Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models | |
| OSI | Osi/0.108.11 Osi/0.108.9 Osi/0.108.8 |
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. | |
| OVITO | OVITO/3.12.4-basic OVITO/3.7.11-basic |
OVITO is a scientific visualization and data analysis solution for atomistic and other particle-based models. It helps scientists gain meaningful and quick insights from numerical simulation results. | |
| P11-KIT | p11-kit/0.25.3 |
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. | |
| P3DFFT | p3dfft/20250416-7b70d9a |
P3DFFT stands for Parallel Three-Dimensional Fast Fourier Transforms. It is a library for large-scale computer simulations on parallel platforms. | |
| P4VASP | P4VASP/20180428 |
P4VASP is an open-source 3D visualization tool for the VASP molecular dynamics and computational chemistry software package. | |
| 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. | |
| PAIRTOOLS | pairtools/1.1.2 pairtools/1.1.0 |
pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. pairtools perform various operations on Hi-C pairs and occupy the middle position in a typical Hi-C data processing pipeline. | |
| PAL2NAL | PAL2NAL/14 |
PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) subs- titution rates. | |
| PAML | PAML/4.10.7 PAML/4.10.5 |
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | |
| PANDOC | Pandoc/3.6.2 |
If you need to convert files from one markup format into another, pandoc is your swiss-army knife | |
| PANGO | Pango/1.54.0 Pango/1.51.0 Pango/1.50.14 Pango/1.50.12 Pango/1.50.7 Pango/1.48.5 |
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. | |
| PAPI | PAPI/7.0.1 |
PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. | |
| PARABRICKS | Parabricks/4.5.0 Parabricks/4.0.1 |
Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generatio n sequencing DNA and RNA data. | HPRC Docs |
| PARAFOLD | ParaFold/2.0-CUDA-11.7.0 |
This project is a modified version of DeepMind's AlphaFold2 to achieve high-throughput protein structure prediction. | |
| PARALLEL | parallel/20240322 parallel/20230722 parallel/20220722 parallel/20210722 parallel/ |
parallel: Build and execute shell commands in parallel | |
| PARALLEL-HASHMAP | Parallel-Hashmap/1.3.12 |
Parallel Hashmap is built on a modified version of Abseil's flat_hash_map. Parallel Hashmap has lower space requirements, is nearly as fast as the underlying flat_hash_map, and can be used from multiple threads with high levels of concurrency. | |
| PARAMETERIZED | parameterized/0.9.0 |
Parameterized testing with any Python test framework | |
| PARAMIKO | paramiko/3.5.1 paramiko/3.2.0 paramiko/3.1.0 paramiko/2.7.2 |
Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol, providing both client and server functionality. It provides the foundation for the high-level SSH library Fabric, which is what we recommend you use for common client use-cases such as running remote shell commands or transferring files. | |
| PARASAIL | parasail/2.6.2 parasail/2.5 |
parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. | |
| PARAVIEW | ParaView/5.13.2 ParaView/5.13.2-MPI-Linux-Python3.10 ParaView/5.11.2 ParaView/5.10.1-mpi ParaView/5.9.1-mpi |
ParaView is a scientific parallel visualizer. | |
| 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. | |
| PATCHELF | patchelf/0.18.0 patchelf/0.17.2 |
PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. | |
| PAUP | PAUP/4.0a168-centos64 |
PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees. | |
| PCRE | PCRE/8.45 PCRE/8.44 |
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. | |
| PCRE2 | PCRE2/10.45 PCRE2/10.43 PCRE2/10.42 PCRE2/10.40 PCRE2/10.36 |
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 |
PDAL is Point Data Abstraction Library. It is a C/C++ open source library and applications for translating and processing point cloud data. It is not limited to LiDAR data, although the focus and impetus for many of the tools in the library have their origins in LiDAR. | |
| PEAR | PEAR/0.9.11 |
PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. | |
| PERL | Perl/5.40.0 Perl/5.38.2 Perl/5.38.0 Perl/5.36.1 Perl/5.36.0 Perl/5.36.0-minimal Perl/5.34.1 Perl/5.34.1-minimal Perl/5.34.0 Perl/5.32.1 Perl/5.30.2 |
Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. | |
| PERL-BUNDLE-CPAN | Perl-bundle-CPAN/5.40.0 Perl-bundle-CPAN/5.38.2 Perl-bundle-CPAN/5.38.0 Perl-bundle-CPAN/5.36.1 |
A set of common packages from CPAN | |
| PETSC | PETSc/3.22.5 PETSc/3.20.3 PETSc/3.20.3-debug PETSc/3.19.2-64bit PETSc/3.17.4 |
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. | |
| PGAP | PGAP/2025-05-06.build7983 |
The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). | |
| PGENOMICS | pgenomics/1.0.1 |
pgenomics is a bundle of software modules for use with plant genomics workflows. | |
| PGGB | PGGB/0.7.4 |
pggb: the PanGenome Graph Builder A pangenome variation graph is a kind of generic multiple sequence alignment. It lets us understand any kind of sequence variation between a collection of genomes. It shows us similarity where genomes walk through the same parts of the graph, and differences where they do not. pggb generates this kind of graph using an all-to-all alignment of input sequences (wfmash), graph induction (seqwish), and progressive normalization (smoothxg, gfaffix). After construction, pggb generates diagnostic visualizations of the graph (odgi). A variant call report (in VCF) representing both small and large variants can be generated based on any reference genome included in the graph (vg). pggb writes its output in GFAv1 format, which can be used as input by numerous "genome graph" and pangenome tools, such as the vg and odgi toolkits. pggb has been tested at scale in the Human Pangenome Reference Consortium (HPRC) as a method to build a graph from the draft human pangenome. | |
| PHIERCC | pHierCC/1.27 pHierCC/1.24 |
HierCC is a multi-level clustering scheme for population assignments based on core genome Multi-Locus Sequence Types (cgMLSTs). | |
| PHOBIUS | Phobius/1.01 |
Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. | |
| PHONO3PY | phono3py/3.15.1 phono3py/2.7.0 |
A simulation package of phonon-phonon interaction related properties. | |
| PHONOPY | phonopy/2.38.2 phonopy/2.20.0 |
Phonopy is an open source package of phonon calculations based on the supercell approach. | |
| PICARD | picard/3.0.0-Java-17 picard/2.25.1-Java-11 |
A set of tools (in Java) for working with next generation sequencing data in the BAM format. | |
| PICRUST2 | PICRUSt2/2.6.2 PICRUSt2/2.6.1 |
PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. | |
| PIGZ | pigz/2.8 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. | HPRC Docs |
| PILLOW-SIMD | Pillow-SIMD/10.4.0 Pillow-SIMD/9.5.0 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 | |
| PINT | Pint/0.23 |
Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units. | |
| PIPENV | pipenv/2025.0.2 |
Pipenv is a Python virtualenv management tool that supports a multitude of systems and nicely bridges the gaps between pip, python (using system python, pyenv or asdf) and virtualenv. Pipenv automatically creates and manages a virtualenv for your projects, as well as adds/removes packages from your Pipfile as you install/uninstall packages. | |
| PIXI | pixi/0.59.0 |
A universal Conda package builder for Windows, macOS and Linux (like conda-build but faster). | |
| PIXMAN | pixman/0.46.2 pixman/0.43.4 pixman/0.42.2 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/2.3.0 pkgconf/2.2.0 pkgconf/2.0.3 pkgconf/1.9.5 pkgconf/1.9.3 pkgconf/1.8.0 |
pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. | |
| PLINK | PLINK/2.00a3.7 |
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | |
| PLOTLY-ORCA | plotly-orca/1.3.1 |
Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line. | |
| PLOTLY.PY | plotly.py/6.3.1 plotly.py/5.24.1 plotly.py/5.18.0 plotly.py/5.16.0 plotly.py/5.12.0 |
An open-source, interactive graphing library for Python | |
| PLUMED | PLUMED/2.9.3 PLUMED/2.9.2 PLUMED/2.9.0 PLUMED/2.8.1 PLUMED/2.8.0 PLUMED/2.8.0-PyTorch-1.12.1-CUDA-11.4.1 |
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. | |
| PMIX | PMIx/5.0.6 PMIx/5.0.2 PMIx/4.2.6 PMIx/4.2.4 PMIx/4.2.2 PMIx/4.1.2 PMIx/4.1.0 PMIx/3.2.3 PMIx/3.1.5 |
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. | |
| PNETCDF | PnetCDF/1.14.0 PnetCDF/1.13.0 PnetCDF/1.12.3 |
Parallel netCDF: A Parallel I/O Library for NetCDF File Access | |
| POCL | pocl/4.0 pocl/1.8 |
PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported). | |
| POD5-FILE-FORMAT | pod5-file-format/0.3.10 |
POD5 is a file format for storing nanopore dna data in an easily accessible way. The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format. | |
| POETRY | poetry/2.1.2 poetry/1.8.3 poetry/1.7.1 poetry/1.6.1 poetry/1.5.1 poetry/1.2.2 poetry/1.1.7 poetry/1.1.6 poetry/1.1.3 |
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. | |
| POGENOM | POGENOM/0.8.4 |
POGENOM (POpulation GENOmics from Metagenomes) is a computer program that calculates several population genomic parameters for a genome in relation to a set of metagnome samples. | |
| POLARS | polars/1.28.1 polars/0.47.1 polars/0.20.2 |
Polars is a blazingly fast DataFrame library for manipulating structured data. The core is written in Rust and this module provides its interface for Python. | |
| POPPLER | poppler/24.04.0 |
Poppler is a PDF rendering library | |
| PORTMIDI | PortMidi/2.0.4 |
PortMidi is a library for software developers. It supports real-time input and output of MIDI data using a system-independent interface. PortMidi runs on Windows (using MME), Macintosh (using CoreMIDI), and Linux (using ALSA). | |
| POSTGRESQL | PostgreSQL/16.4 PostgreSQL/16.1 PostgreSQL/14.4 |
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. | HPRC Docs |
| 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. | |
| 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. | |
| 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. | |
| PRECICE | preCICE/2.5.0 |
preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations, including, but not restricted to fluid-structure interaction and conjugate heat transfer simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. This allows for the high flexibility that is needed to keep a decent time-to-solution for complex multi-physics scenarios. | |
| PRESEQ | preseq/3.2.0 |
Software for predicting library complexity and genome coverage in high-throughput sequencing. | |
| PRESTO | presto/1.0.0-20230501-R-4.4.2 |
Presto performs a fast Wilcoxon rank sum test and auROC 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. | |
| PROJ | PROJ/9.4.1 PROJ/9.3.1 PROJ/9.2.0 PROJ/9.1.1 PROJ/9.0.0 PROJ/8.0.1 |
Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates | |
| PROKKA | prokka/1.14.5 |
Prokka is a software tool for the rapid annotation of prokaryotic genomes. | |
| PROTHINT | ProtHint/2.6.0 |
ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences. | |
| PROTOBUF | protobuf/28.0 protobuf/25.3 protobuf/24.0 protobuf/23.0 protobuf/3.19.4 protobuf/3.17.3 |
Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data. | |
| PROTOBUF-PYTHON | protobuf-python/5.28.0 protobuf-python/4.25.3 protobuf-python/4.24.0 protobuf-python/4.23.0 protobuf-python/3.19.4 protobuf-python/3.17.3 |
Python Protocol Buffers runtime library. | |
| PRRTE | PRRTE/3.0.8 PRRTE/3.0.5 |
PRRTE is the PMIx Reference RunTime Environment | |
| PSMC | psmc/0.6.5_20221121 |
This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. | |
| PSUTIL | psutil/7.0.0 psutil/6.1.0 psutil/6.0.0 psutil/5.9.8 psutil/5.9.3 psutil/5.8.0 psutil/5.7.2 |
A cross-platform process and system utilities module for Python | |
| PSYCOPG2 | psycopg2/2.9.9 |
Psycopg is the most popular PostgreSQL adapter for the Python programming language. | |
| PUGIXML | pugixml/1.14 |
pugixml is a light-weight C++ XML processing library | |
| PULLSEQ | pullseq/1.0.2 |
Utility program for extracting sequences from a fasta/fastq file | |
| PULP | PuLP/2.8.0 PuLP/2.7.0 PuLP/2.5.0 |
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. | |
| PV | pv/1.7.24 |
Pipe Viewer - monitor the progress of data through a pipe | |
| PY-CPUINFO | py-cpuinfo/9.0.0 py-cpuinfo/8.0.0 |
py-cpuinfo gets CPU info with pure Python. | |
| PY3DMOL | py3Dmol/2.1.0 py3Dmol/2.0.1.post1 |
A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook. | |
| PYBEDTOOLS | pybedtools/0.11.0 pybedtools/0.10.0 pybedtools/0.9.1 pybedtools/0.9.0 |
pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. | |
| PYBIGWIG | pyBigWig/0.3.24 pyBigWig/0.3.23 pyBigWig/0.3.22 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 | pybind11/2.13.6 pybind11/2.12.0 pybind11/2.11.1 pybind11/2.10.3 pybind11/2.9.2 pybind11/2.9.2-Python-2.7.18 pybind11/2.7.1 pybind11/2.6.2 pybind11/2.6.0 |
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. | |
| 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/1.25.0 PyCairo/1.24.0 PyCairo/1.21.0 |
Python bindings for the cairo library | |
| PYCURL | PycURL/7.45.2 |
PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features. | |
| PYDANTIC | pydantic/2.9.1 pydantic/2.7.4 pydantic/2.5.3 pydantic/1.10.13 pydantic/1.10.4 |
Data validation and settings management using Python type hinting. | |
| PYDICOM | pydicom/2.4.4 |
Pure python package for DICOM medical file reading and writing. | |
| PYEM | pyem/0.5-CUDA-12.2.0 pyem/0.5-CUDA-11.7.0 |
UCSF pyem is a collection of Python modules and command-line utilities for electron microscopy of biological samples. | |
| PYFAIDX | pyfaidx/0.8.1.2 pyfaidx/0.8.1.1 pyfaidx/0.7.2.2 pyfaidx/0.7.1 |
pyfaidx: efficient pythonic random access to fasta subsequences | |
| PYFFTW | pyFFTW/0.15.1 pyFFTW/0.13.1 |
A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. | |
| PYGAME | pygame/2.5.2 |
Pygame is a set of Python modules designed for writing video games. Pygame adds functionality on top of the excellent SDL library. This allows you to create fully featured games and multimedia programs in the python language. | |
| PYGENOMETRACKS | pyGenomeTracks/3.8 |
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. | |
| PYGEOS | PyGEOS/0.14 |
PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance improvement when operating on arrays of geometries. | |
| PYGOBJECT | PyGObject/3.46.0 PyGObject/3.44.1 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. | |
| PYGRAPHVIZ | pygraphviz/1.10 |
PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms. | |
| PYPROJ | pyproj/3.6.0 |
Python interface to PROJ4 library for cartographic transformations | |
| PYQT-BUILDER | PyQt-builder/1.15.4 |
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 | PyQt5/5.15.10 PyQt5/5.15.7 PyQt5/5.15.5 |
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. | |
| PYROSETTA | PyRosetta/4.release-387 |
PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. | |
| PYSAM | Pysam/0.22.1 Pysam/0.22.0 Pysam/0.21.0 Pysam/0.20.0 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. | |
| PYSPOA | pyspoa/0.2.1 |
Python bindings to spoa. | |
| PYTABLES | PyTables/3.9.2 PyTables/3.8.0 |
PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. | |
| PYTEST-FLAKEFINDER | pytest-flakefinder/1.1.0 |
Runs tests multiple times to expose flakiness. | |
| PYTEST-RERUNFAILURES | pytest-rerunfailures/15.0 pytest-rerunfailures/14.0 pytest-rerunfailures/12.0 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-SUBTESTS | pytest-subtests/0.13.1 |
unittest subTest() support and subtests fixture. | |
| PYTHIA | PYTHIA/8.314 PYTHIA/8.314-noROOT PYTHIA/8.309 PYTHIA/8.309-noROOT |
PYTHIA is a program for the generation of high-energy physics collision events, i.e. for the description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original research, but also borrows many formulae and other knowledge from the literature. As such it is categorized as a general purpose Monte Carlo event generator. | |
| PYTHON | Python/3.13.1 Python/3.12.3 Python/3.11.5 Python/3.11.3 Python/3.10.8 Python/3.10.8-bare Python/3.10.4 Python/3.10.4-bare Python/3.9.6 Python/3.9.6-bare Python/3.9.5 Python/3.9.5-bare Python/3.8.6 Python/2.7.18 Python/2.7.18-bare |
Python is a programming language that lets you work more quickly and integrate your systems more effectively. | HPRC Docs |
| PYTHON-BUNDLE-PYPI | Python-bundle-PyPI/2025.04 Python-bundle-PyPI/2024.06 Python-bundle-PyPI/2023.10 Python-bundle-PyPI/2023.06 |
Bundle of Python packages from PyPI | |
| PYTHON-IGRAPH | python-igraph/0.11.9 python-igraph/0.11.8 python-igraph/0.11.4-CUDA-12.1.1 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/1.6.1 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/1.3.4 python-parasail/1.2.4 |
Python Bindings for the Parasail C Library | |
| PYTMHMM | pyTMHMM/1.3.6 |
pyTMHMM is a Python 3.5+/Cython implementation of the transmembrane helix predictor using a hidden Markov model (TMHMM) | |
| PYTORCH | PyTorch/2.7.0 PyTorch/2.6.0 PyTorch/2.1.2 PyTorch/2.1.2-CUDA-12.1.1 PyTorch/2.0.1 PyTorch/1.13.1 PyTorch/1.12.1-CUDA-11.7.0 PyTorch/1.12.1-CUDA-11.4.1 PyTorch/1.12.0-CUDA-11.7.0 |
Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. | HPRC Docs |
| PYTORCH-BUNDLE | PyTorch-bundle/2.1.2-CUDA-12.1.1 |
PyTorch with compatible versions of official Torch extensions. | |
| PYTORCH-GEOMETRIC | PyTorch-Geometric/2.5.0-PyTorch-2.1.2-CUDA-12.1.1 |
PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. | |
| PYYAML | PyYAML/6.0.2 PyYAML/6.0.1 PyYAML/6.0 PyYAML/5.4.1 |
PyYAML is a YAML parser and emitter for the Python programming language. | |
| PYZMQ | PyZMQ/25.1.2 PyZMQ/25.1.1 |
Python bindings for ZeroMQ | |
| QCHEM | qchem/6.3.0-openmp qchem/5.4.2-openmp qchem/5.4.0-openmp qchem/5.3.2-openmp |
Q-Chem 6.3.0 release environment module | |
| 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. | |
| QIIME2 | QIIME2/2025.7-Amplicon QIIME2/2024.10-Metagenome QIIME2/2024.10-Pathogenome QIIME2/2024.10-Amplicon QIIME2/2023.2 |
QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. | |
| QISKIT | Qiskit/2.0.2 |
Qiskit is an open-source SDK for working with quantum computers at the level of extended quantum circuits, operators, and primitives. | |
| QT5 | Qt5/5.15.16 Qt5/5.15.13 Qt5/5.15.10 Qt5/5.15.7 Qt5/5.15.5 Qt5/5.15.2 |
Qt is a comprehensive cross-platform C++ application framework. | |
| QT6 | Qt6/6.9.3 Qt6/6.7.2 Qt6/6.6.3 Qt6/6.5.2 |
Qt is a comprehensive cross-platform C++ application framework. | |
| QUANTUMESPRESSO | QuantumESPRESSO/7.4.1-NVHPC-24.9-CUDA-12.6.0 QuantumESPRESSO/7.4 |
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). | HPRC Docs |
| QUAST | QUAST/5.3.0 QUAST/5.2.0 |
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. | |
| QUICKTREE | QuickTree/2.5 |
QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. | |
| QWT | Qwt/6.3.0 Qwt/6.2.0 |
The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. | |
| R | R/4.4.2 R/4.4.1 R/4.3.2 R/4.2.2 R/4.2.1 |
R is a free software environment for statistical computing and graphics. | HPRC Docs |
| R-BUNDLE-BIOCONDUCTOR | R-bundle-Bioconductor/3.20-R-4.4.2 R-bundle-Bioconductor/3.19-R-4.4.1 R-bundle-Bioconductor/3.18-R-4.3.2 R-bundle-Bioconductor/3.16-R-4.2.2 R-bundle-Bioconductor/3.15-R-4.2.1 |
Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. | |
| R-BUNDLE-CRAN | R-bundle-CRAN/2024.11 R-bundle-CRAN/2024.06 R-bundle-CRAN/2023.12 R-bundle-CRAN/2023.12-abind |
Bundle of R packages from CRAN | |
| RACON | Racon/1.5.0 |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. | |
| RAGTAG | RagTag/2.1.0 |
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: homology-based misassembly correction, homology-based assembly scaffolding and patching, and scaffold merging. RagTag also provides command line utilities for working with common genome assembly file formats. | |
| RAPIDJSON | RapidJSON/1.1.0-20240815 RapidJSON/1.1.0-20240409 RapidJSON/1.1.0-20230928 RapidJSON/1.1.0 |
A fast JSON parser/generator for C++ with both SAX/DOM style API | |
| RAPSEARCH2 | RAPSearch2/2.24 |
RAPSearch stands for Reduced Alphabet based Protein similarity Search | |
| RATTLER-BUILD | rattler-build/0.49.0 |
A universal Conda package builder for Windows, macOS and Linux (like conda-build but faster). | |
| RAXML | RAxML/8.2.12-pthreads-sse3 |
RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. | |
| RAXML-NG | RAxML-NG/1.2.0 |
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. | |
| RAY-PROJECT | Ray-project/2.37.0 Ray-project/2.6.2 |
Ray is a fast and simple framework for building and running distributed applications. | |
| RE2 | RE2/2024-07-02 RE2/2024-03-01 RE2/2023-08-01 RE2/2023-03-01 RE2/2022-06-01 |
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. | |
| RE2C | re2c/4.2 re2c/3.1 re2c/3.0 re2c/2.2 re2c/2.1.1 |
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. | |
| RECON | RECON/1.08 |
Patched version of RECON to be used with RepeatModeler. | |
| REDIS | Redis/7.4.1 Redis/7.0.8 |
Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster. | |
| REDIS-PY | redis-py/5.1.1 redis-py/4.5.1 |
The Python interface to the Redis key-value store. | |
| RELERNN | ReLERNN/1.0.0-CUDA-11.7.0 |
ReLERNN uses deep learning to infer the genome-wide landscape of recombination from as few as four individually sequenced chromosomes, or from allele frequencies inferred by pooled sequencing. | |
| RELION | RELION/5.0.0-CUDA-12.1.1 |
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/4.1.8 RepeatMasker/4.1.7-p1 RepeatMasker/4.1.5 RepeatMasker/4.1.4 |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | |
| REPEATMODELER | RepeatModeler/2.0.6 |
RepeatModeler is a de novo transposable element (TE) family identification and modeling package. | |
| REPEATSCOUT | RepeatScout/1.0.7 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 ) | |
| RJAGS | rjags/4-13-R-4.2.1 |
The rjags package is an interface to the JAGS library. | |
| RMATS-TURBO | rMATS-turbo/4.3.0 |
rMATS turbo is the C/Cython version of rMATS (refer to https://rnaseq-mats.sourceforge.io). | |
| RMBLAST | RMBlast/2.14.1 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. | |
| RNAMMER | RNAmmer/1.2 |
This is an example description. | |
| ROARY | Roary/3.13.0 |
Rapid large-scale prokaryote pan genome analysis | |
| ROCKSDB | RocksDB/10.2.1 |
A Persistent Key-Value Store for Flash and RAM Storage | |
| ROHAN | ROHan/20240903 |
ROHan: inference of heterozygosity rates and runs of homozygosity for modern and ancient samples ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity. ROHan can work on modern and ancient samples with signs of ancient DNA damage. | |
| ROOT | ROOT/6.30.06 ROOT/6.28.12 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. | |
| ROSETTA | Rosetta/3.14 Rosetta/3.14-mpi |
Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. | |
| RPMREBUILD | rpmrebuild/2.18 |
rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use | |
| RSEM | RSEM/1.3.3 |
RNA-Seq by Expectation-Maximization | |
| RUAMEL.YAML | ruamel.yaml/0.18.6 ruamel.yaml/0.17.32 ruamel.yaml/0.17.21 |
ruamel.yaml is a YAML 1.2 loader/dumper package for Python. | |
| RUBY | Ruby/3.4.2 Ruby/3.3.0 Ruby/3.2.2 |
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/1.86.0 Rust/1.86.0-nightly Rust/1.85.1 Rust/1.83.0 Rust/1.81.0 Rust/1.79.0 Rust/1.78.0 Rust/1.76.0 Rust/1.75.0 Rust/1.75.0-nightly Rust/1.73.0 Rust/1.70.0 Rust/1.65.0 Rust/1.60.0 Rust/1.54.0 Rust/1.52.1 Rust/nightly-20250326 |
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. | |
| RUSTWORKX | rustworkx/0.16.0 rustworkx/0.15.1 |
rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take advantage of the performance and safety that Rust provides. It is designed to provide a high performance general purpose graph library for any Python application. | |
| SALMID | SalmID/0.1.23 |
Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia). | |
| SALMON | Salmon/1.10.3 Salmon/1.9.0 |
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimate from RNA-seq data. | |
| SAMBAMBA | Sambamba/0.7.1 |
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. | |
| SAMBLASTER | samblaster/0.1.26 |
samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. | |
| SAMTOOLS | SAMtools/1.21 SAMtools/1.20 SAMtools/1.19.2 SAMtools/1.18 SAMtools/1.17 SAMtools/1.16.1 SAMtools/1.13 SAMtools/1.10 SAMtools/0.1.20 |
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. | |
| SAS | SAS/9.4 |
a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics. | HPRC Docs |
| SCAFACOS | ScaFaCoS/1.0.4 |
ScaFaCoS is a library of scalable fast coulomb solvers. | |
| SCALAPACK | ScaLAPACK/2.2.2-fb ScaLAPACK/2.2.0-fb ScaLAPACK/2.1.0 ScaLAPACK/2.1.0-fb |
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. | |
| SCALENE | Scalene/1.5.26 |
Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while delivering far more detailed information. | |
| SCANPY | scanpy/1.10.4 scanpy/1.9.8 |
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. | |
| SCHRODINGER | Schrodinger/2024-4 Schrodinger/2023-4 Schrodinger/2023-1 |
Schrodinger software is a physics-based computational platform that integrates differentiated solutions for predictive modeling, data analytics, and collaboration to enable rapid exploration of chemical space. | HPRC Docs |
| SCIKIT-BIO | scikit-bio/0.6.0 |
scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. | |
| SCIKIT-BUILD | scikit-build/0.18.1 scikit-build/0.17.6 scikit-build/0.17.2 scikit-build/0.16.7 scikit-build/0.15.0 scikit-build/0.14.1 scikit-build/0.11.1 |
Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. | |
| SCIKIT-BUILD-CORE | scikit-build-core/0.11.1 scikit-build-core/0.10.6 scikit-build-core/0.9.3 scikit-build-core/0.5.0 |
Scikit-build-core is a complete ground-up rewrite of scikit-build on top of modern packaging APIs. It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake. | |
| SCIKIT-IMAGE | scikit-image/0.24.0 scikit-image/0.22.0 scikit-image/0.19.3 |
scikit-image is a collection of algorithms for image processing. | |
| SCIKIT-LEARN | scikit-learn/1.7.0 scikit-learn/1.6.1 scikit-learn/1.5.2 scikit-learn/1.4.2 scikit-learn/1.4.0 scikit-learn/1.3.2 scikit-learn/1.3.1 scikit-learn/1.2.1 scikit-learn/1.1.2 scikit-learn/0.24.2 scikit-learn/0.23.2 scikit-learn/0.20.4 scikit-learn/0.20.4-Python-2.7.18 |
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. | HPRC Docs |
| SCIPY-BUNDLE | SciPy-bundle/2025.06 SciPy-bundle/2024.06-Python-2.7.18 SciPy-bundle/2024.05 SciPy-bundle/2024.05-CDMS SciPy-bundle/2023.11 SciPy-bundle/2023.07 SciPy-bundle/2023.02 SciPy-bundle/2022.05 SciPy-bundle/2021.10 SciPy-bundle/2021.05 SciPy-bundle/2020.11 |
Bundle of Python packages for scientific software | |
| SCOARY | Scoary/1.6.16 |
Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. | |
| SCONS | SCons/4.6.0 SCons/4.4.0 |
SCons is a software construction tool. | |
| SCOTCH | SCOTCH/7.0.6 SCOTCH/7.0.4 SCOTCH/7.0.3 SCOTCH/7.0.1 SCOTCH/6.1.0 |
Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. | |
| SCRIPTS_FOR_GB | Scripts_for_GB/2019.02.24 |
Scripts for: The pipeline used to detect gene conversion events. The pipeline used to compute Ka, Ks, and Ka/Ks for duplicated gene pairs. The pipeline used to compute Pearson correlation coefficients (r) between expression profiles of the two gene copies. The pipline used to infer the Ks peaks corresponding to WGD events | |
| SDL2 | SDL2/2.32.8 SDL2/2.30.6 SDL2/2.28.5 SDL2/2.28.2 SDL2/2.26.3 SDL2/2.0.22 |
SDL: Simple DirectMedia Layer, a cross-platform multimedia library | |
| SDL2_IMAGE | SDL2_image/2.8.2 |
This is a simple library to load images of various formats as SDL surfaces. It can load BMP, GIF, JPEG, LBM, PCX, PNG, PNM (PPM/PGM/PBM), QOI, TGA, XCF, XPM, and simple SVG format images. It can also load AVIF, JPEG-XL, TIFF, and WebP images, depending on build options (see the note below for details.) | |
| SDL2_MIXER | SDL2_mixer/2.8.0 |
Due to popular demand, here is a simple multi-channel audio mixer. It supports 8 channels of 16 bit stereo audio, plus a single channel of music. It can load FLAC, MP3, Ogg, VOC, and WAV format audio. It can also load MIDI, MOD, and Opus audio, depending on build options (see the note below for details.) | |
| SDL2_TTF | SDL2_ttf/2.22.0 |
This library is a wrapper around the FreeType and Harfbuzz libraries, allowing you to use TrueType fonts to render text in SDL applications. | |
| SDSL-LITE | sdsl-lite/2.1.1 sdsl-lite/2.0.3 |
The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic lower bound of the object while supporting operations of the original object efficiently. The theoretical time complexity of an operation performed on the classical data structure and the equivalent succinct data structure are (most of the time) identical. | |
| SEABORN | Seaborn/0.13.2 Seaborn/0.12.2 Seaborn/0.12.1 |
Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. | |
| SEMIBIN | SemiBin/2.1.0-CUDA-11.7.0 |
SemiBin: Metagenomic Binning Using Siamese Neural Networks for short and long reads | |
| SENTENCEPIECE | SentencePiece/0.2.0 SentencePiece/0.1.97 |
Unsupervised text tokenizer for Neural Network-based text generation. | |
| SENTIEON-CLI | Sentieon-CLI/1.4.0 |
A command-line interface for the Sentieon software | |
| SEPP | SEPP/4.5.5 SEPP/4.5.1 |
SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. | |
| SEQAN | SeqAn/2.4.0 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/2.9.0 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. | |
| SEQSERO2 | SeqSero2/1.3.2 |
SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies | |
| SEQTK | seqtk/1.4 |
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. | |
| 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 | |
| SETTARG | settarg/ |
The settarg module provides a way to connect the loaded modules with your build system by setting environment variables. | |
| SETUPTOOLS | setuptools/80.9.0 setuptools/75.6.0 setuptools/69.5.1 setuptools/57.4.0 setuptools/56.2.0 setuptools/50.3.0 setuptools/44.1.1 |
Easily download, build, install, upgrade, and uninstall Python packages | |
| SETUPTOOLS-RUST | setuptools-rust/1.11.0 setuptools-rust/1.9.0 setuptools-rust/1.8.0 setuptools-rust/1.6.0 setuptools-rust/0.12.1 |
setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython. | |
| SEURATDISK | SeuratDisk/20231104-R-4.4.2 |
Interfaces for HDF5-based Single Cell File Formats | |
| SFLD | SFLD/1.1 |
SFLD is a database of protein families based on hidden Markov models (HMMs). | |
| SHAP | SHAP/0.47.0 SHAP/0.46.0 SHAP/0.43.0 |
SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions. | |
| SHAPEIT5 | SHAPEIT5/20240315 |
Segmented HAPlotype Estimation and Imputation Tools version 5 (SHAPEIT5) SHAPEIT5 estimates haplotypes in large datasets, with a special focus on rare variants. | |
| SHAPELY | Shapely/2.0.1 Shapely/1.8.2 |
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. | |
| SIESTA | Siesta/4.1.5 |
SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. | |
| SIGNALP | SignalP/4.1f |
SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | |
| SIMPLE-DFTD3 | Simple-DFTD3/1.2.1 |
Reimplementation of the D3 dispersion correction. The s-dftd3 project aims to provide a user-friendly and uniform interface to the D3 dispersion model and for the calculation of DFT-D3 dispersion corrections. | |
| SINGULAR | Singular/4.4.0 |
Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. | |
| SIP | SIP/6.8.1 |
SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. | |
| SKANI | skani/0.2.2 |
skani - accurate, fast nucleotide identity calculation for MAGs, genomes, and databases | |
| SMCPP | smcpp/20231219 |
SMC++ is a program for estimating the size history of populations from whole genome sequence data. | |
| SMETANA | SMETANA/1.2.1 |
Species METabolic interaction ANAlysis (SMETANA) is a python-based command line tool to analyse microbial communities. It takes as input a microbial communtity (from a collection of genome-scale metabolic models in SBML format) and computes of several metrics that describe the potential for cross-feeding interactions between community members. | |
| SMITHWATERMAN | smithwaterman/20160702 |
smith-waterman-gotoh alignment algorithm. | |
| SMRT-LINK | SMRT-Link/25.2.0.266456-cli-tools-only SMRT-Link/13.1.0.221970-cli-tools-only |
PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided | |
| SMV | SMV/6.10.5 |
Smokeview is a visualization program that displays output of FDS and CFAST simulations. | |
| SNAKEMAKE | snakemake/8.4.2 snakemake/7.32.3 snakemake/7.22.0 |
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. | |
| SNAP-HMM | SNAP-HMM/20221022 |
SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. | |
| SNAPATAC2 | SnapATAC2/2.8.0 |
Single-cell epigenomics analysis tools | |
| SNAPPY | snappy/1.2.2 snappy/1.2.1 snappy/1.1.10 snappy/1.1.9 snappy/1.1.8 |
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. | |
| SNIFFLES | Sniffles/2.6.1 |
A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data. | |
| SNOSCAN | Snoscan/1.0 |
Search for C/D box methylation guide snoRNA genes in a genomic sequence. | |
| SNPEFF | snpEff/5.2c-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). | |
| SOAPDENOVO2 | SOAPdenovo2/r242 |
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. | |
| SOX | SoX/14.4.2 |
Sound eXchange, the Swiss Army knife of audio manipulation | |
| SPACERANGER | SpaceRanger/2.1.1 |
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. | |
| SPADES | SPAdes/4.2.0 SPAdes/4.0.0 SPAdes/3.15.5 SPAdes/3.15.4 |
Genome assembler for single-cell and isolates data sets | |
| 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. | |
| SPARK | Spark/3.5.1-Java-17 |
Spark is Hadoop MapReduce done in memory | |
| 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. | |
| SPGLIB-PYTHON | spglib-python/2.5.0 spglib-python/2.1.0 spglib-python/2.0.0 |
Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. | |
| SPOA | spoa/4.1.0 |
Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences | |
| SPORTS1.1 | SPORTS1.1/2025.01.16 |
Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs | |
| SPYTHON | spython/0.3.13 |
Singularity Python (spython) is the Python API for working with Singularity containers. | |
| SQLALCHEMY | SQLAlchemy/2.0.25 |
SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language. | |
| SQLITE | SQLite/3.47.2 SQLite/3.45.3 SQLite/3.43.1 SQLite/3.42.0 SQLite/3.39.4 SQLite/3.38.3 SQLite/3.36 SQLite/3.35.4 |
SQLite: SQL Database Engine in a C Library | |
| SRA-TOOLKIT | SRA-Toolkit/3.2.0 SRA-Toolkit/3.1.1 SRA-Toolkit/3.0.10 SRA-Toolkit/3.0.3 |
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/3.3.2-Java-11 |
Single Read Paired Read Indel Substitution Minimizer | |
| 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. | |
| STACKS | Stacks/2.66 |
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. | |
| STAR | STAR/2.7.11b STAR/2.7.11a STAR/2.7.10b STAR/2.7.2b |
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. | |
| STAR-CCM+ | STAR-CCM+/20.04.008 STAR-CCM+/20.04.008-R8 STAR-CCM+/19.06.008 STAR-CCM+/19.06.008-R8 STAR-CCM+/19.04.009 STAR-CCM+/19.04.009-R8 STAR-CCM+/19.02.013 STAR-CCM+/19.02.013-R8 STAR-CCM+/18.02.010 STAR-CCM+/18.02.010-R8 STAR-CCM+/17.02.008 STAR-CCM+/17.02.008-R8 |
Software for solving problems involving flow (of fluids or solids), heat transfer and stress. - Homepage: http://www.cd-adapco.com/products/star-ccm | |
| STATA | Stata/18 Stata/17 |
Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. | HPRC Docs |
| STATA-MIGRATION_GROUP | Stata-migration_group/17 |
Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. | |
| STATA-XCEN_GROUP | Stata-xcen_group/17 |
Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. | |
| STATISTICS-R | Statistics-R/0.34 |
Perl interface with the R statistical program | |
| STATSMODELS | statsmodels/0.14.5 statsmodels/0.14.4 statsmodels/0.14.1 statsmodels/0.14.0 |
Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. | |
| STRAINY | Strainy/1.2 |
Strainy is a tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). | |
| STRINGTIE | StringTie/3.0.1 StringTie/2.2.3 StringTie/2.2.1 |
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts | |
| STRUCTURE | Structure/2.3.4 |
The program structure is a free software package for using multi-locus genotype data to investigate population structure. | |
| SUBPHASER | SubPhaser/1.2.6 |
SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers | |
| SUBREAD | Subread/2.0.8 |
High performance read alignment, quantification and mutation discovery | |
| SUBVERSION | Subversion/1.14.2 |
Subversion is an open source version control system. | |
| SUITESPARSE | SuiteSparse/7.10.1 SuiteSparse/7.7.0 SuiteSparse/7.1.0 SuiteSparse/5.13.0-METIS-5.1.0 |
SuiteSparse is a collection of libraries to manipulate sparse matrices. | |
| SUNDIALS | SUNDIALS/6.7.0 |
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers | |
| SUPERLU_DIST | SuperLU_DIST/8.2.1 SuperLU_DIST/8.1.2 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. | |
| SUPERNOVA | Supernova/2.1.1 |
Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances. Almost all other methods instead merge homologous chromosomes into single incorrect 'consensus' sequences. Supernova is the only practical method for creating diploid assemblies of large genomes. | |
| SWAK4FOAM | swak4Foam/20190219-OpenFOAM-6-20190620 swak4Foam/20190219-OpenFOAM-6 |
swak4Foam stands for SWiss Army Knife for Foam. Like that knife it rarely is the best tool for any given task, but sometimes it is more convenient to get it out of your pocket than going to the tool-shed to get the chain-saw. | |
| SWIG | SWIG/4.2.1 SWIG/4.1.1 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. | |
| SYRI | SyRI/1.7.0 |
Synteny and Rearrangement Identifier (SyRI). | |
| SZIP | Szip/2.1.1 |
Szip compression software, providing lossless compression of scientific data | |
| TABIXPP | tabixpp/1.1.2 |
C++ wrapper to tabix indexer | |
| TAXATOR-TK | taxator-tk/1.5.0-Python-2.7.18 |
A set of programs for the taxonomic analysis of nucleotide sequence data | |
| TBB | tbb/2021.13.0 tbb/2021.11.0 tbb/2021.5.0 tbb/2020.3 |
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/20230713 tbl2asn/20230713-linux64 tbl2asn/20220427-linux64 |
Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank | |
| TCL | Tcl/8.6.16 Tcl/8.6.14 Tcl/8.6.13 Tcl/8.6.12 Tcl/8.6.11 |
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. | |
| TCLAP | TCLAP/1.4.0-rc2 TCLAP/1.2.5 |
TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was initially inspired by the user friendly CLAP library. | |
| TCSH | tcsh/6.24.13 tcsh/6.24.10 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. | |
| TECPLOT | tecplot/2024r1 |
Tecplot is graphics package that can handle large data sets, automate workflows, and visualize parametric results. | |
| TENSORBOARD | tensorboard/2.18.0 tensorboard/2.15.1 tensorboard/2.13.0 tensorboard/2.11.1 |
TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs. | |
| TENSORBOARDX | tensorboardX/2.6.2.2 |
Tensorboard for PyTorch. | |
| TENSORFLOW | TensorFlow/2.18.1 TensorFlow/2.15.1 TensorFlow/2.15.1-CUDA-12.1.1 TensorFlow/2.13.0 TensorFlow/2.11.0 TensorFlow/2.11.0-CUDA-11.7.0 |
An open-source software library for Machine Intelligence | HPRC Docs |
| TENSORSTORE | tensorstore/0.1.65 tensorstore/0.1.60 |
TensorStore is an open-source C++ and Python software library designed for storage and manipulation of large multi-dimensional arrays. | |
| TESMALL | TEsmall/2.0.8 |
A pipeline for profiling TE-derived small RNAs. | |
| TEST-DRIVE | test-drive/0.5.0 |
This project offers a lightweight, procedural unit testing framework based on nothing but standard Fortran. | |
| 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. | |
| THERMO-CALC | Thermo-Calc/2024.2 Thermo-Calc/2024.1 Thermo-Calc/2023.2 Thermo-Calc/2023.1 Thermo-Calc/2022.2 Thermo-Calc/2022.1 Thermo-Calc/2021.2 Thermo-Calc/2021.1 |
Thermocalc is a software package for thermodynamic calculations. It is widely used for a variety of calculations. | |
| TIGMINT | Tigmint/1.2.10 |
Correct misassemblies in genome assembly drafts using linked or long sequencing reads | |
| TIME | time/1.9 |
The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running. | |
| TK | Tk/8.6.16 Tk/8.6.14 Tk/8.6.13 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/3.13.1 Tkinter/3.12.3 Tkinter/3.11.5 Tkinter/3.11.3 Tkinter/3.10.8 Tkinter/3.10.4 |
Tkinter module, built with the Python buildsystem | |
| TLDR | tldr/1.2.2-2025.07.06 |
Transposons from Long DNA Reads | |
| TLPARSE | tlparse/0.3.37 |
Parse structured PT2 (PyTorch 2) logs | |
| TMHMM | TMHMM/2.0c |
Prediction of transmembrane helices in proteins. | |
| TOKENIZERS | tokenizers/0.21.4 tokenizers/0.15.2 tokenizers/0.3.0 |
Fast State-of-the-Art Tokenizers optimized for Research and Production | |
| TOML-FORTRAN | TOML-Fortran/0.4.2 |
TOML parser for Fortran projects | |
| TOPAZ | topaz/0.2.5.20231120-CUDA-12.1.1 |
Particle picking software for single particle cryo-electron microscopy using convolutional neural networks and positive-unlabeled learning. Includes methods for micrograph denoising. | |
| TORNADO | tornado/6.4.1 tornado/6.4 tornado/6.3.2 |
Tornado is a Python web framework and asynchronous networking library. | |
| TQDM | tqdm/4.67.1 tqdm/4.66.5 tqdm/4.66.2 tqdm/4.66.1 tqdm/4.64.1 tqdm/4.64.0 |
A fast, extensible progress bar for Python and CLI | |
| TRANSDECODER | TransDecoder/5.7.1 |
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. | |
| TRF | TRF/4.09.1 |
Tandem Repeats Finder: a program to analyze DNA sequences. | |
| TRF2GFF | TRF2GFF/20241225 |
Converts Tandem Repeat Finder .dat file output into GFF3 format. | |
| TRIMAL | trimAl/1.4.1 |
EVB, FEP and LIE simulator. | |
| TRIMMOMATIC | Trimmomatic/0.39-Java-17 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. | |
| TRIM_GALORE | 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). | |
| TRINITY | Trinity/2.15.2 Trinity/2.15.2-Java-17 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/4.0.2 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). | |
| TRNASCAN-SE | tRNAscan-SE/2.0.12 |
tRNAscan-SE is the most widely employed tool for identifying and annotating tRNA genes in genomes. | |
| TSEBRA | TSEBRA/1.1.2.5 TSEBRA/1.1.2.5-long_reads |
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 BRAKER1 and BRAKER2 predicitons to increase their accuracies. | |
| TURM | turm/0.7.3 |
A text-based user interface (TUI) for the Slurm Workload Manager, which provides a convenient way to manage your cluster jobs. | |
| TWISTED | Twisted/22.4.0 |
Twisted is an event-based framework for internet applications, supporting Python 3.6+. | |
| TWL-NINJA | TWL-NINJA/1.00-cluster_only TWL-NINJA/0.98-cluster_only |
Nearly Infinite Neighbor Joining Application. | |
| UCC | UCC/1.3.0 UCC/1.2.0 UCC/1.1.0 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. | |
| UCC-CUDA | UCC-CUDA/1.3.0-CUDA-12.6.0 UCC-CUDA/1.0.0-CUDA-11.7.0 |
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. This module adds the UCC CUDA support. | |
| UCX | UCX/1.18.0 UCX/1.16.0 UCX/1.15.0 UCX/1.14.1 UCX/1.13.1 UCX/1.12.1 UCX/1.11.2 UCX/1.10.0 UCX/1.8.0 |
Unified Communication X An open-source production grade communication framework for data centric and high-performance applications | |
| UCX-CUDA | UCX-CUDA/1.16.0-CUDA-12.6.0 UCX-CUDA/1.15.0-CUDA-12.4.1 UCX-CUDA/1.15.0-CUDA-12.4.0 UCX-CUDA/1.14.1-CUDA-12.1.1 UCX-CUDA/1.12.1-CUDA-11.7.0 UCX-CUDA/1.11.2-CUDA-11.4.1 |
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. | |
| UMAP-LEARN | umap-learn/0.5.7 umap-learn/0.5.5 |
Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. | |
| UNIDECODE | Unidecode/1.3.6 |
Python library for lossy ASCII transliterations of Unicode text (port of Text::Unidecode Perl module) | |
| 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. | |
| UNIFRAC | UniFrac/1.4 |
UniFrac is the de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in both double and single precision (fp32). This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. | |
| UNIMAP | unimap/0.1 |
Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi-part index and short-read mapping. Its long-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment. | |
| UNITTEST-XML-REPORTING | unittest-xml-reporting/3.1.0 |
A unittest test runner that can save test results to XML files in xUnit format. The files can be consumed by a wide range of tools, such as build systems, IDEs and continuous integration servers. | |
| 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. | |
| USEARCH | USEARCH/11.0.667-i86linux32 |
USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST. | |
| UTF8PROC | utf8proc/2.9.0 utf8proc/2.8.0 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/2.41 util-linux/2.40 util-linux/2.39 util-linux/2.38.1 util-linux/2.38 util-linux/2.37 util-linux/2.36 |
Set of Linux utilities | |
| UV | uv/0.9.7 |
An extremely fast Python package and project manager, written in Rust. | |
| VALGRIND | Valgrind/3.23.0 Valgrind/3.21.0 |
Valgrind: Debugging and profiling tools | |
| VARSCAN | VarScan/2.4.4-Java-11 |
Variant calling and somatic mutation/CNV detection for next-generation sequencing data | |
| VASP | vasp/6.3.2 vasp/6.3.2-VTST-195-VASPsol-libbeef vasp/5.4.4.pl2 vasp/5.4.4.pl2-VTST-195-VASPsol-Wannier90-libbeef |
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP 6.3.2 - Homepage: http://www.vasp.at | HPRC Docs |
| VCFLIB | vcflib/1.0.9-R-4.3.2 |
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. | |
| 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. | |
| VCONTACT2 | vConTACT2/0.11.3 |
vConTACT2 is a tool to perform guilt-by-contig-association classification of viral genomic sequence data. | |
| VERKKO | Verkko/2.2.1 |
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads. | |
| VG | VG/1.65.0 |
variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods | |
| VIBRANT | VIBRANT/1.2.1 |
Virus Identification By iteRative ANnoTation | |
| VIRALRECALL | ViralRecall/2.1 |
ViralRecall is a flexible command-line tool for detecting signatures of giant viruses (NCLDV) in genomic data. | |
| VIRSORTER2 | VirSorter2/2.2.4 |
VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. | |
| VIRTUALENV | virtualenv/20.29.2 virtualenv/20.26.2 virtualenv/20.24.6 virtualenv/20.23.1 virtualenv/20.7.0 virtualenv/20.4.6 virtualenv/20.0.34 |
A tool for creating isolated virtual python environments. | |
| VIRTUALGL | VirtualGL/3.1 |
VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration. | |
| VISIT | Visit/3.4.1 Visit/3.2.1 |
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (<101 core) desktop-sized projects to large (>105 core) leadership-class computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations. VisIt contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured, adaptive and unstructured meshes. Owing to its customizeable plugin design, VisIt is capabable of visualizing data from over 120 different scientific data formats. | |
| VMD | VMD/1.9.4a57 VMD/1.9.4a57-no-truecolor VMD/1.9.4a57-CUDA-11.8.0-OptiX-6.5.0-no-truecolor |
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | HPRC Docs |
| 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. | |
| VSEARCH | VSEARCH/2.30.0 VSEARCH/2.25.0 |
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. | |
| VT | vt/0.57721 |
A tool set for short variant discovery in genetic sequence data. | |
| VTK | VTK/9.3.0 VTK/9.2.6 VTK/9.2.2 |
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. | |
| WANDB | wandb/0.20.1 wandb/0.16.1 |
CLI and Python API for Weights and Biases (wandb), a tool for visualizing and tracking your machine learning experiments. | |
| WAYLAND | Wayland/1.23.92 Wayland/1.23.0 Wayland/1.22.0 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+/2.41.4 |
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. | |
| WEBLOGO | weblogo/2.8.2 |
WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. | |
| WEBPROXY | WebProxy/0000 |
WebProxy module sets up web and ftp roxy environment variables, http_proxy, https_proxy, and ftp_proxy, for internet acceess from the compute nodes. Wiki page: https://hprc.tamu.edu/wiki/SW:WebProxy | HPRC Docs |
| WFA2 | WFA2/2.3.4 |
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. | |
| WGET | wget/1.25.0 wget/1.24.5 wget/1.21.4 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. | |
| WHATSHAP | WhatsHap/2.2 |
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. | |
| WINNOWMAP | Winnowmap/2.03 |
Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques. | |
| WPEBACKEND-FDO | wpebackend-fdo/1.15.90 |
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. | |
| WPS | WPS/4.4-dmpar |
WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. | |
| WRAPT | wrapt/1.16.0 wrapt/1.15.0 wrapt/1.14.1 |
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. | |
| WRF | WRF/4.6.1-dmpar WRF/4.4-dmpar |
The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. | HPRC Docs |
| WXPYTHON | 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/3.2.2.1 |
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. | |
| X11 | X11/20250521 X11/20240607 X11/20231019 X11/20230603 X11/20221110 X11/20220504 X11/20210802 X11/20210518 |
The X Window System (X11) is a windowing system for bitmap displays | |
| X264 | x264/20250619 x264/20240513 x264/20231019 x264/20230226 x264/20220620 x264/20210613 x264/20210414 |
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 | x265/4.1 x265/3.6 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. | |
| XARRAY | xarray/2024.5.0 |
xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. | |
| XERCES-C++ | Xerces-C++/3.2.5 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/3.1.3 XlsxWriter/3.0.8 |
A Python module for creating Excel XLSX files | |
| XML-LIBXML | XML-LibXML/2.0210 XML-LibXML/2.0209 XML-LibXML/2.0208 XML-LibXML/2.0207 |
Perl binding for libxml2 | |
| XMLF90 | xmlf90/1.6.3 |
A fast XML parser and generator in Fortran | |
| XORG-MACROS | xorg-macros/1.20.2 xorg-macros/1.20.1 xorg-macros/1.20.0 xorg-macros/1.19.3 xorg-macros/1.19.2 |
X.org macros utilities. | |
| XPROP | xprop/1.2.8 xprop/1.2.7 xprop/1.2.6 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/6.7.1 |
xtb - An extended tight-binding semi-empirical program package. | |
| XVFB | Xvfb/21.1.14 Xvfb/21.1.9 Xvfb/21.1.8 Xvfb/21.1.6 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. | |
| XXD | xxd/9.1.1275 xxd/9.1.0307 xxd/9.0.2112 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. | |
| XZ | XZ/5.6.3 XZ/5.4.5 XZ/5.4.4 XZ/5.4.2 XZ/5.2.7 XZ/5.2.5 |
xz: XZ utilities | |
| YACS | YACS/0.1.8 |
YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These "configurations" typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network. | |
| YAHS | YaHS/1.2.2 |
YaHS is a scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. | |
| YASM | Yasm/1.3.0 |
Yasm: Complete rewrite of the NASM assembler with BSD license | |
| Z3 | Z3/4.13.4 Z3/4.13.0 Z3/4.12.2 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. | |
| ZEBULON | ZEBULON/z912 ZEBULON/z904 |
Zébulon is the state-of-the-art finite element solver of the Z-set suite. - Homepage: http://www.zset-software.com/products/zebulon/ | HPRC Docs |
| ZEROMQ | ZeroMQ/4.3.5 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. | |
| ZLIB | zlib/1.3.1 zlib/1.2.13 zlib/1.2.12 zlib/1.2.11 |
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/1.5.6 zstd/1.5.5 zstd/1.5.2 zstd/1.5.0 zstd/1.4.9 |
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. |