Software Modules on the FASTER Cluster
ACES Software Modules FASTER Software Modules Grace Software Modules
(Last Updated: Jul 24, 2025)
| Name | Versions available | Description | Notes |
|---|---|---|---|
| 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 |
| ABINIT | ABINIT/9.6.2 ABINIT/9.4.2 ABINIT/9.2.1 |
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. | |
| ABRICATE | ABRicate/1.0.0 ABRicate/0.9.9 |
Mass screening of contigs for antimicrobial and virulence genes | |
| ABSEIL | Abseil/20240722.0 Abseil/20240116.1 Abseil/20230802.1 Abseil/20230125.3 Abseil/20230125.2 Abseil/20210324.2 |
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/0.10.0 |
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 ABySS/2.1.5 |
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | |
| ACTC | ACTC/1.1 |
ACTC converts independent triangles into triangle strips or fans. | |
| ADAPTERREMOVAL | AdapterRemoval/2.3.3 |
AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. | |
| ADEPT-2 | Adept-2/20231208 |
A combined array and automatic differentiation library in C++. | |
| ADMIXTURE | ADMIXTURE/1.3.0 |
ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. | |
| AESARA | aesara/2.8.9 |
Aesara is a Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. | |
| AFLOW | AFLOW/3.2.11 |
Automatic FLOW for Materials Discovery | |
| AGAT | AGAT/0.9.2 |
Suite of tools to handle gene annotations in any GTF/GFF format. | |
| AGENT | AGEnt/0.3.1 |
AGEnt is a program for identifying accessory genomic elements in bacterial genomes by using an in-silico subtractive hybridization approach against a core genome, such as those generated by the Spine algorithm. | |
| AIOHTTP | aiohttp/3.9.5 aiohttp/3.8.5 aiohttp/3.8.3 aiohttp/3.8.1 |
Asynchronous HTTP client/server framework for asyncio and Python. | |
| ALITV | AliTV/20231212 |
Visualize whole genome alignments as linear maps. | |
| ALIVIEW | AliView/1.28 |
AliView is yet another alignment viewer and editor, but this is probably one of the fastest and most intuitive to use, not so bloated and hopefully to your liking. | |
| ALLHIC | ALLHiC/0.9.14 |
Genome scaffolding based on Hi-C data | |
| ALPHAFOLD | AlphaFold/2023.07.24-CUDA-11.7.0-sokrypton-ColabFold AlphaFold/2.3.1-CUDA-11.7.0 AlphaFold/2.2.2-CUDA-11.3.1 AlphaFold/2.1.1 |
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known. This package of AlphaFold from git repo sokrypton contains patches for ColabFold. | 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/1.2.8 |
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/20-CUDA-11.4.1-Python-3.9.5 Amber/20-CUDA-11.4.1-NCCL-2.11.4-Python-3.9.5 |
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 |
| AMBERTOOLS | AmberTools/22.3 AmberTools/21.12 |
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. | |
| AMOS | AMOS/3.1.0 |
The AMOS consortium is committed to the development of open-source whole genome assembly software | |
| AMPHORA2 | AMPHORA2/20190730-Java-13-pthreads-avx2 |
An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences. | |
| AMPLPY | amplpy/0.13.3 |
An interface that allows developers to access the features of AMPL from within Python. | |
| ANACONDA3 | Anaconda3/2024.02-1 Anaconda3/2023.07-2 Anaconda3/2023.03-1 Anaconda3/2022.10 Anaconda3/2022.05 Anaconda3/2021.11 Anaconda3/2021.05 Anaconda3/2020.11 Anaconda3/2020.07 Anaconda3/2019.10 |
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 angsd/0.935 angsd/0.925 |
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. | |
| ANNOSINE | AnnoSINE/2024.01.16 |
SINE Annotation Tool for Plant Genomes | |
| ANNOVAR | ANNOVAR/20200607-Perl-5.36.0 ANNOVAR/20200607-Perl-5.34.0 |
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/2024R2 ANSYS/2023R2 ANSYS/2022R2 ANSYS/2021R2 |
ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. | HPRC Docs |
| ANSYSEM | 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-11 ant/1.10.11-Java-11 ant/1.10.9-Java-11 ant/1.10.8-Java-11 ant/1.10.5-Java-1.8 |
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-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 | |
| AOCC | AOCC/3.1.0 |
AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0 | |
| APR | APR/1.7.0 |
Apache Portable Runtime (APR) libraries. | |
| APR-UTIL | APR-util/1.6.1 |
Apache Portable Runtime (APR) util libraries. | |
| ARAGORN | ARAGORN/1.2.38 |
a program to detect tRNA genes and tmRNA genes in nucleotide sequences | |
| ARCADE-LEARNING-ENVIRONMENT | Arcade-Learning-Environment/0.8.1 Arcade-Learning-Environment/0.7.3 |
The Arcade Learning Environment (ALE) is a simple framework that allows researchers and hobbyists to develop AI agents for Atari 2600 games. It is built on top of the Atari 2600 emulator Stella and separates the details of emulation from agent design. This video depicts over 50 games currently supported in the ALE. | |
| ARCHIVE-ZIP | Archive-Zip/1.68 |
Provide an interface to ZIP archive files. | |
| ARCHSPEC | archspec/0.2.1 archspec/0.1.4 archspec/0.1.3 archspec/0.1.0-Python-3.8.6 archspec/0.1.0-Python-3.8.2 archspec/0.1.0-Python-3.7.4 |
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. | |
| ARIA2 | aria2/1.35.0 |
aria2-1.15.1: Multi-threaded, multi-protocol, flexible download accelerator | |
| ARMADILLO | Armadillo/12.8.0 Armadillo/12.6.2 Armadillo/11.4.3 Armadillo/10.7.5 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-ng/3.7.0 |
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | |
| ARROW | Arrow/16.1.0 Arrow/14.0.1 Arrow/11.0.0 Arrow/8.0.0 Arrow/6.0.0 Arrow/0.17.1 |
Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. | |
| ARROW-R | arrow-R/16.1.0-R-4.4.1 arrow-R/8.0.0-R-4.2.1 arrow-R/6.0.0.2-R-4.1.2 |
R interface to the Apache Arrow C++ library | |
| ARVIZ | ArviZ/0.11.4 |
Exploratory analysis of Bayesian models with Python | |
| ASE | ASE/3.22.1 ASE/3.20.1 ASE/3.20.1-Python-3.8.2 ASE/3.20.1-Python-3.7.4 ASE/3.19.0-Python-3.8.2 ASE/3.19.0-Python-3.7.4 |
ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed. | |
| ASSEMBLYTICS | Assemblytics/1.2.1 |
Assemblytics: a web analytics tool for the detection of variants from an assembly | |
| ASSIMP | 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. | |
| ASTROPY | astropy/5.2.2 astropy/5.1.1 astropy/5.0.4 astropy/4.3.1 |
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-spi2-atk/2.34.2 at-spi2-atk/2.34.1 |
AT-SPI 2 toolkit bridge | |
| AT-SPI2-CORE | at-spi2-core/2.50.0 at-spi2-core/2.49.91 at-spi2-core/2.46.0 at-spi2-core/2.44.1 at-spi2-core/2.40.3 at-spi2-core/2.40.2 at-spi2-core/2.38.0 at-spi2-core/2.36.0 at-spi2-core/2.34.0 |
Assistive Technology Service Provider Interface. | |
| ATK | ATK/2.38.0 ATK/2.36.0 ATK/2.34.1 |
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. | |
| ATOMEYE | Atomeye/20220830 |
AtomEye is free atomistic visualization software for all major UNIX platforms. | |
| ATTR | attr/2.5.2 attr/2.5.1 attr/2.4.48 |
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/3.4.0 |
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 AutoDock-GPU/1.5.3-CUDA-11.3.1 |
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. | |
| AUTODOCK-VINA | AutoDock-Vina/1.1.2-linux_x86 |
AutoDock Vina is an open-source program for doing molecular docking. | |
| AUTOMAKE | Automake/1.16.5 Automake/1.16.4 Automake/1.16.3 Automake/1.16.2 Automake/1.16.1 |
Automake: GNU Standards-compliant Makefile generator | |
| AUTOTOOLS | Autotools/20231222 Autotools/20220317 Autotools/20210726 Autotools/20210128 Autotools/20200321 Autotools/20180311 |
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool | |
| AWKWARD | awkward/1.7.0 |
Awkward Array is a library for nested, variable-sized data, including arbitrary-length lists, records, mixed types, and missing data, using NumPy-like idioms. | |
| AWSCLI | awscli/2.13.37 awscli/2.11.21 awscli/2.0.55-Python-3.8.2 |
Universal Command Line Environment for AWS | |
| AXL | axl/20220413 |
A C/C++ project support library that covers specialized needs for compiler/parser writing, asynchronous IO, device management, cryptography, etc. | |
| BALI-PHY | BAli-Phy/3.6.1 BAli-Phy/3.6.0 |
Software that estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. It uses likelihood-based evolutionary models of substitutions and insertions and deletions to place gaps. | |
| BAMKIT | bamkit/2017.04.12 |
Tools for common BAM file manipulations | |
| BAMTOOLS | BamTools/2.5.2 BamTools/2.5.1 |
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. | |
| BANDAGE | Bandage/0.9.0 Bandage/0.8.1_Centos |
Bandage is a program for visualising de novo assembly graphs | |
| BAZEL | Bazel/6.3.1 Bazel/6.1.0 Bazel/5.1.1 Bazel/4.2.2 Bazel/3.7.2 Bazel/3.6.0 Bazel/2.0.0 Bazel/0.29.1 Bazel/0.26.1 |
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/39.13 BBMap/39.08 BBMap/39.06 BBMap/39.01 BBMap/38.98 BBMap/38.96 BBMap/38.90 |
BBMap short read aligner, and other bioinformatic tools. | |
| BCBIO-GFF | bcbio-gff/0.7.0 |
Read and write Generic Feature Format (GFF) with Biopython integration. | |
| BCFTOOLS | BCFtools/1.20 BCFtools/1.19 BCFtools/1.18 BCFtools/1.17 BCFtools/1.14 BCFtools/1.11 BCFtools/1.10.2 |
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 | Beagle/5.4.22Jul22.46e-Java-11 |
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. | |
| BEAGLE-LIB | beagle-lib/4.0.0 beagle-lib/4.0.0-CUDA-11.7.0 beagle-lib/3.1.2 |
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/2.7.3 Beast/2.7.3-CUDA-11.7.0 Beast/2.6.7 |
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 BeautifulSoup/4.9.1-Python-3.8.2 |
Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. | |
| BEDOPS | BEDOPS/2.4.26 |
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/2.29.2 |
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. | |
| BERKELEY-UPC | Berkeley-UPC/2022.10.0 |
Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware. The programmer is presented with a single shared, partitioned address space, where variables may be directly read and written by any processor, but each variable is physically associated with a single processor. | |
| BINDCRAFT | BindCraft/1.5.1-CUDA-12.1.1 |
Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. | |
| BINUTILS | 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/2.31.1 binutils/2.30 binutils/2.28 binutils/2.27 binutils/2.26 |
binutils: GNU binary utilities | |
| BIO-DB-HTS | Bio-DB-HTS/3.01 |
Read files using HTSlib including BAM/CRAM, Tabix and BCF database files | |
| 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-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. | |
| BIO-TABLE | bio-table/1.0.0-Ruby-3.0.1 |
bio-table is the swiss knife of tabular data. Tables of data are often used in bioinformatics, especially in conjunction with Excel spreadsheets and DB queries. | |
| BIOAWK | bioawk/1.0 |
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. | |
| BIOM-FORMAT | biom-format/2.1.14 biom-format/2.1.12 |
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/1.7.7 BioPerl/1.7.2 |
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/1.78 Biopython/1.78-Python-3.8.2 Biopython/1.77-Python-3.7.4 Biopython/1.76-Python-2.7.18 Biopython/1.75-Python-3.7.4 Biopython/1.75-Python-2.7.16 |
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/3.0.5 Bison/3.0.4 |
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/2.11.0-Linux_x86_64 |
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. | |
| BLAST+ | BLAST+/2.16.0 BLAST+/2.14.1 BLAST+/2.14.0 BLAST+/2.13.0 BLAST+/2.12.0 BLAST+/2.11.0 BLAST+/2.10.1 BLAST+/2.9.0 BLAST+/2.2.31 |
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/3.5 |
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | |
| BLENDER | Blender/3.1.2-linux-x64 Blender/3.0.0-linux-x64 |
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/3.1-amd BLIS/2.2-amd BLIS/1.0 BLIS/0.9.0 BLIS/0.8.1 BLIS/0.8.0 |
AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. | |
| BLOSC | Blosc/1.21.5 Blosc/1.21.3 Blosc/1.21.0 Blosc/1.17.1 |
Blosc, an extremely fast, multi-threaded, meta-compressor library | |
| BLOSC2 | Blosc2/2.13.2 Blosc2/2.8.0 Blosc2/2.6.1 Blosc2/2.4.3 |
Blosc, an extremely fast, multi-threaded, meta-compressor library | |
| BMTAGGER | bmtagger/3.101 |
Best Match Tagger for removing human reads from metagenomics datasets | |
| BOHRIUM | bohrium/0.11.0.post60 |
Bohrium provides automatic acceleration of array operations in Python/NumPy, C, and C++ targeting multi-core CPUs and GP-GPUs. Forget handcrafting CUDA/OpenCL to utilize your GPU and forget threading, mutexes and locks to utilize your multi-core CPU. | |
| BOKEH | bokeh/3.4.1 bokeh/3.2.2 bokeh/3.2.1 bokeh/2.4.3 bokeh/2.4.2 bokeh/2.4.1 bokeh/2.2.3 bokeh/2.0.2-Python-3.8.2 bokeh/1.4.0-Python-3.7.4 |
Statistical and novel interactive HTML plots for Python | |
| BONSAI | Bonsai/0.5.1 |
Bonsai: Flexible Taxonomic Analysis and Extension | |
| BOOST | 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/1.74.0 Boost/1.72.0 Boost/1.72.0-no_mpi Boost/1.71.0 Boost/1.55.0 |
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/1.82.0 Boost.Python/1.81.0 Boost.Python/1.77.0 Boost.Python/1.76.0 Boost.Python/1.74.0 Boost.Python/1.71.0 |
Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. | |
| BOTO3 | boto3/1.28.70 boto3/1.26.163 |
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. | |
| BOTORCH | BoTorch/0.6.0-Python-3.8.6 |
GPyTorch is a Gaussian process library implemented using PyTorch. | |
| BOTTLENECK | Bottleneck/1.3.2-Python-3.9.6 Bottleneck/1.3.2-Python-3.8.6 Bottleneck/1.3.2-Python-3.8.2 |
Fast NumPy array functions written in C | |
| BOWTIE | Bowtie/1.3.1 Bowtie/1.3.0 Bowtie/1.2.3 |
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 Bowtie2/2.4.4 Bowtie2/2.4.2 Bowtie2/2.4.1 Bowtie2/2.3.5.1 |
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/2.9 Bracken/2.7 |
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. | |
| BREAKDANCER | BreakDancer/1.4.5 |
BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads | |
| 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. | |
| 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 | |
| BUILD | build/1.0.3 build/0.10.0 |
A simple, correct Python build frontend. | |
| BUILDENV | buildenv/default |
This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show |
|
| BUSCO | BUSCO/5.7.1 BUSCO/5.1.2 |
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. | |
| BWIDGET | bwidget/1.9.15 bwidget/1.9.14 |
The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. | |
| BX-PYTHON | bx-python/0.10.0 bx-python/0.9.0 bx-python/0.8.13 |
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 bzip2/1.0.6 |
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/1.18.1 c-ares/1.17.2 |
c-ares is a C library for asynchronous DNS requests (including name resolves) | |
| 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. | |
| CANU | canu/2.2 canu/2.1.1-Java-1.8 |
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing | |
| CAP3 | CAP3/2015.02.10 |
CAP3 assembly program | |
| CAPNPROTO | CapnProto/1.0.1.1 CapnProto/0.10.2 CapnProto/0.9.1 CapnProto/0.7.0 |
Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. | |
| CAPSTONE | Capstone/5.0.3capstone/5.0.1 |
Capstone is a disassembly framework with the target of becoming the ultimate disasm engine for binary analysis and reversing in the security community. | |
| CARTOPY | Cartopy/0.22.0 Cartopy/0.20.3 Cartopy/0.20.0 |
Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy. | |
| 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 | Catch2/3.4.0 Catch2/2.13.10 Catch2/2.13.9 |
Catch2 is mainly a unit testing framework for C++, but it also provides basic micro-benchmarking features, and simple BDD macros. | |
| 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. | |
| CBC | 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. | |
| CBLAS | CBLAS/20110120 |
C interface to the BLAS | |
| CCACHE | ccache/4.9 ccache/4.6.1 |
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/4.8.1-maxlen10M |
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. | |
| CDAT | CDAT/8.2.1-Python-3.8.2 |
CDAT is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for data analysis problems. | |
| CDBFASTA | CDBfasta/1.0.0 |
CDB (Constant DataBase) indexing and retrieval tools for FASTA files | |
| CDO | CDO/1.9.10 |
CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. | |
| CELLPROFILER | CellProfiler/4.2.8 |
CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. | |
| 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. | |
| CELLRANGER-ATAC | CellRanger-ATAC/2.1.0 |
Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. | |
| 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. | |
| 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/1.16.0 cffi/1.15.1 cffi/1.14.5 |
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/3.49 |
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. | |
| CGAL | CGAL/5.6.1 CGAL/5.6 CGAL/5.5.2 CGAL/5.2 CGAL/4.14.3 CGAL/4.14.3-Python-3.8.2 CGAL/4.14.1-Python-3.7.4 |
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/1.1.5 |
Core genome Multi-Locus Sequence Typing | |
| CHAPEL | Chapel/1.29.0-mpi |
Chapel is a programming language designed for productive parallel computing at scale. | |
| CHARLIECLOUD | charliecloud/0.33 charliecloud/0.31 |
Charliecloud provides user-defined software stacks (UDSS) for high-performance computing (HPC) centers. | HPRC Docs |
| CHECK | Check/0.15.2check/0.15.2 |
A unit testing framework for C. | |
| CHECKM | CheckM/1.2.2 CheckM/1.1.3-Python-3.8.2 CheckM/1.0.18-Python-2.7.18 |
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. | |
| CHIMERA | Chimera/1.15 |
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. | |
| CHIMERAX | ChimeraX/2022.02.22 ChimeraX/1.7.1 ChimeraX/1.7 ChimeraX/1.6.1 ChimeraX/1.5 ChimeraX/1.4 ChimeraX/1.3 ChimeraX/1.2.5 |
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. | |
| CHIMES | ChIMES/1.0.2 |
The Chebyshev Interaction Model for Efficient Simulation (ChIMES) is a machine-learned interatomic potential that can target chemical reactivity. ChIMES models are able to approach quantum-accuracy through a systematically improvable explicitly many-bodied basis comprised of linear combinations of Chebyshev polynomials. | |
| 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 |
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | |
| CLANG | Clang/16.0.6 Clang/16.0.6-CUDA-12.1.1 Clang/13.0.1 Clang/13.0.1-CUDA-11.7.0 Clang/13.0.1-CUDA-11.4.1 Clang/12.0.1 Clang/11.0.1 Clang/9.0.1 |
C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. | |
| CLANG-AOMP | Clang-AOMP/4.5.0 |
AOMP is an open source Clang/LLVM based compiler with added support for the OpenMP® API on Radeon™ GPUs. | |
| CLAPACK | CLAPACK/3.2.1 |
C version of LAPACK | |
| CLARABEL.RS | Clarabel.rs/0.7.1 |
Interior-point solver for convex conic optimisation problems in Rust. | |
| CLHEP | CLHEP/2.4.6.4 CLHEP/2.4.5.1 |
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/1.17.9 Clp/1.17.8 Clp/1.17.7 |
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/3.29.3 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/3.11.4 CMake/3.9.1 |
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | |
| CMSEQ | CMSeq/1.0.4 |
CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus. | |
| CNVNATOR | CNVnator/0.4.1 |
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads | |
| COBAYA | cobaya/3.2.2 |
Cobaya (code for bayesian analysis) is a framework for sampling and statistical modelling: it allows you to explore an arbitrary prior or posterior using a range of Monte Carlo samplers (including the advanced MCMC sampler from CosmoMC, and the advanced nested sampler PolyChord). | |
| CODE-SERVER | code-server/4.93.1 code-server/4.90.2 code-server/4.19.1 code-server/4.9.1 code-server/4.8.3 code-server/4.5.1 |
Run VS Code on any machine anywhere and access it in the browser. | |
| CODINGQUARRY | CodingQuarry/2.0 |
Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts | |
| COGSOFT | COGsoft/3.4.6 |
Software for making Clusters of Orthologous Groups | |
| COINUTILS | CoinUtils/2.11.10 CoinUtils/2.11.9 CoinUtils/2.11.6 |
CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. | |
| COLABFOLD | ColabFold/1.3.0-CUDA-11.3.1 |
Making Protein folding accessible to all! | |
| COMPLEASM | Compleasm/0.2.7 |
Copleasm: a faster and more accurate reimplementation of BUSCO. | |
| COMPRESS-RAW-ZLIB | Compress-Raw-Zlib/2.202 |
Low-Level Interface to zlib or zlib-ng compression library | |
| CONAN | conan/1.58.0 |
Decentralized, open-source (MIT), C/C++ package manager. | |
| CONCOCT | CONCOCT/1.1.0-Python-2.7.18 |
Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. | |
| CONFIGURABLE-HTTP-PROXY | configurable-http-proxy/4.6.1 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/3.0.2 CoordgenLibs/3.0.1 |
Schrodinger-developed 2D Coordinate Generation | |
| COREUTILS | Coreutils/9.1 Coreutils/8.32 |
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/0.6.1 |
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. | |
| CP2K | CP2K/2023.1 CP2K/2023.1-CUDA-11.8.0 CP2K/8.2 |
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. | |
| CPIO | cpio/2.15 |
The cpio package contains tools for archiving. | |
| CPPUNIT | CppUnit/1.15.1 |
CppUnit is the C++ port of the famous JUnit framework for unit testing. | |
| CPPY | cppy/1.2.1 cppy/1.1.0 |
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. | |
| CPPZMQ | cppzmq/4.9.0 |
cppzmq is a C++ binding for libzmq. | |
| CROMWELL | cromwell/85-Java-11 |
Cromwell is a Workflow Management System geared towards scientific workflows. | |
| CRYPTOGRAPHY | cryptography/42.0.8 cryptography/41.0.5 cryptography/41.0.1 cryptography/3.4.7 |
cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. | |
| CSBLAST | csblast/2.2.3-Linux64 |
CS-BLAST for context-specific protein sequence searching is a simple extension of BLAST that is able to significantly improve its sensitivity and alignment quality | |
| CTFFIND | ctffind/4.1.14 |
Program for finding CTFs of electron micrographs. | |
| CUDA | CUDA/12.6.0 CUDA/12.5.0 CUDA/12.4.1 CUDA/12.4.0 CUDA/12.3.0 CUDA/12.2.2 CUDA/12.2.0 CUDA/12.1.1 CUDA/12.1.0 CUDA/12.0.0 CUDA/11.8.0 CUDA/11.7.0 CUDA/11.6.0 CUDA/11.5.0 CUDA/11.4.2 CUDA/11.4.1 CUDA/11.3.1 CUDA/11.2.2 CUDA/11.1.1 CUDA/11.0.2 CUDA/10.1.243 CUDA/8.0.61 |
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-SAMPLES | CUDA-Samples/12.1-CUDA-12.1.1 |
Samples for CUDA Developers which demonstrates features in CUDA Toolkit | |
| CUDACORE | CUDAcore/11.4.1 CUDAcore/11.1.1 CUDAcore/11.0.2 |
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. | |
| CUDF | cuDF/23.04.0 |
Built based on the Apache Arrow columnar memory format, cuDF is a GPU DataFrame library for loading, joining, aggregating, filtering, and otherwise manipulating data. | |
| CUDNN | cuDNN/9.4.0.58-CUDA-12.3.0 cuDNN/8.9.2.26-CUDA-12.1.1 cuDNN/8.8.0.121-CUDA-12.0.0 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/8.2.1.32-CUDA-11.3.1 cuDNN/8.1.0.77-CUDA-11.2.2 cuDNN/8.0.4.30-CUDA-11.1.1 cuDNN/8.0.4.30-CUDA-11.0.2 cuDNN/7.6.4.38 |
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. | |
| CUNIT | CUnit/2.1-3 |
Automated testing framework for C. | |
| CUPY | CuPy/11.4.0-CUDA-11.4.1 |
CuPy is an open-source array library accelerated with NVIDIA CUDA. | |
| CURL | cURL/8.7.1 cURL/8.3.0 cURL/8.0.1 cURL/7.86.0 cURL/7.83.0 cURL/7.78.0 cURL/7.76.0 cURL/7.72.0 cURL/7.69.1 cURL/7.66.0 cURL/7.60.0 |
libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. | |
| CUSPARSELT | cuSPARSELt/0.6.0.6-CUDA-12.1.1 cuSPARSELt/0.3.0.3-CUDA-11.4.1 |
NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix | |
| CUSZ | cuSZ/0.3.1 |
A modular error-bounded lossy compression framework for scientific datasets. | |
| CUTADAPT | cutadapt/5.0 cutadapt/4.9 cutadapt/4.2 cutadapt/3.5 cutadapt/3.4 cutadapt/3.4-Python-3.8.2 cutadapt/2.10-Python-3.8.2 cutadapt/2.7-Python-3.7.4 cutadapt/1.18-Python-2.7.18 |
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 cuTENSOR/1.7.0.1-CUDA-12.0.0 cuTENSOR/1.6.1.5-CUDA-11.7.0 cuTENSOR/1.6.1.5-CUDA-11.4.1 |
The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations. | |
| CUTLASS | CUTLASS/3.4.0-CUDA-12.1.1 CUTLASS/2.11.0-CUDA-11.7.0 |
CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these "moving parts" into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications. | |
| CVXOPT | 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. | |
| CVXPY | CVXPY/1.4.2 |
CVXPY is a Python-embedded modeling language for convex optimization problems. It allows you to express your problem in a natural way that follows the math, rather than in the restrictive standard form required by solvers. | |
| CYTHON | Cython/3.0.10 Cython/3.0.8 Cython/3.0.7 Cython/3.0a5 Cython/0.29.33 Cython/0.29.30 Cython/0.29.23 Cython/0.29.22 |
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). | |
| CYTOOLZ | cytoolz/0.12.0-Python-3.9.6 cytoolz/0.9.0-Python-2.7.16 |
Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries. | |
| DACE | dace/0.14.1 |
DaCe is a fast parallel programming framework that takes code in Python/NumPy and other programming languages, and maps it to high-performance CPU, GPU, and FPGA programs, which can be optimized to achieve state-of-the-art. | |
| DAGMC | DAGMC/3.2.3 |
Direct Accelerated Geometry Monte Carlo (DAGMC) is a software package that allows users to perform Monte Carlo radiation transport directly on CAD models. | |
| DALTON | Dalton/2020.0 |
-------------------------------------------------------------------------------------------------------------------------- Dalton: Dalton/2020.0 -------------------------------------------------------------------------------------------------------------------------- | HPRC Docs |
| DASK | dask/2023.9.2 dask/2023.7.1 dask/2022.10.0 dask/2022.7.0 dask/2022.1.0 dask/2021.9.1 dask/2021.2.0 dask/2.18.1-Python-3.8.2 dask/2.8.0-Python-3.7.4 |
Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. | |
| DATAMASH | datamash/1.7 |
GNU datamash performs basic numeric, textual and statistical operations on input data files | |
| DATASETS | datasets/13.35.0 |
The NCBI Datasets datasets command line tools are datasets and dataformat | |
| 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 | |
| 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. | |
| DBCSR | DBCSR/2.5.0 |
DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations. | |
| DBD-MYSQL | DBD-mysql/4.050 DBD-mysql/4.050-Perl-5.30.0 |
Perl binding for MySQL | |
| DBUS | DBus/1.15.8 DBus/1.15.4 DBus/1.15.2 DBus/1.14.0 DBus/1.13.18 DBus/1.13.12 |
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. | |
| DBUS-GLIB | dbus-glib/0.112 |
D-Bus is a message bus system, a simple way for applications to talk to one another. | |
| DB_FILE | DB_File/1.859 DB_File/1.858 DB_File/1.857 DB_File/1.856 DB_File/1.855 DB_File/1.835 |
Perl5 access to Berkeley DB version 1.x. | |
| DCMTK | DCMTK/3.6.7 |
DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. | |
| DECONA | decona/0.1.2-Python-3.7.4 |
fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads | |
| DEEPDIFF | deepdiff/6.7.1 deepdiff/5.8.1 |
DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. | |
| DEEPTOOLS | deepTools/3.5.5 deepTools/3.5.2 deepTools/3.5.1 |
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. | |
| DEEP_REFERENCE_PARSER | deep_reference_parser/2020.8.5-Python-3.7.4 |
Deep Reference Parser is a Deep Learning Model for recognising references in free text. | |
| 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/0.15.1 |
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/4.5.2 DendroPy/4.5.2-Python-2.7.18 DendroPy/4.4.0 |
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. | |
| DESALT | deSALT/1.5.6 |
deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads | |
| DESMOND | 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 |
| DEVITO | Devito/4.6.1-Python-3.8.2 |
Devito is a domain-specific Language (DSL) and code generation framework for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on multiple computer platforms. | |
| DFT-D3 | DFT-D3/3.2.0 |
DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. | |
| DFTB+ | DFTB+/24.1 DFTB+/24.1noMPI |
DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. | |
| DFTBPLUS | dftbplus/24.1 |
DFTB+ is a fast and efficient versatile quantum mechanical simulation software package. Using DFTB+ you can carry out quantum mechanical atomistic simulations similar to density functional theory but in an approximate way, typically gaining around two orders of magnitude in speed. | |
| DFTD3-LIB | dftd3-lib/0.9 |
This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules. | |
| DFTD4 | dftd4/3.7.0 |
The dftd4 project provides an implementation of the generally applicable, charge dependent London-dispersion correction, termed DFT-D4. | |
| DIALS | DIALS/3.22.1 |
DIALS: Diffraction Integration for Advanced Light Sources | |
| DIAMOND | DIAMOND/2.1.9 DIAMOND/2.1.8 DIAMOND/2.1.0 DIAMOND/2.0.15 DIAMOND/2.0.13 DIAMOND/2.0.11 DIAMOND/2.0.7 DIAMOND/0.9.30 |
Accelerated BLAST compatible local sequence aligner | |
| DISTANGSD | distAngsd/d5a9ecb |
-------------------------------------------------------------------------------------------------------------------------- distAngsd: distAngsd/d5a9ecb -------------------------------------------------------------------------------------------------------------------------- | |
| DLIB | dlib/19.24-CUDA-11.7.0 dlib/19.22-CUDA-11.3.1 |
Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments. | |
| DLPACK | DLPack/0.8 |
DLPack is a stable in-memory data structure for an ndarray system to interact with a variety of frameworks. | |
| DM-HAIKU | dm-haiku/0.0.12-CUDA-12.1.1 dm-haiku/0.0.9-CUDA-11.7.0 |
Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural network library for TensorFlow. | |
| DM-REVERB | dm-reverb/0.2.0 |
Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues. | |
| DM-TREE | dm-tree/0.1.8 dm-tree/0.1.6 dm-tree/0.1.5 |
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. | |
| DMFOLD | DMFold/1.2 |
DMFold (also known as DMFold-Multimer) is a deep learning-based approach to protein complex structure and function prediction built on deep multiple sequence alignments (MSAs). | |
| DMLC-CORE | DMLC-Core/0.5 |
DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries. | |
| DORADO | Dorado/0.6.1-Linux64dorado/0.7.3-Linux64 dorado/0.7.2-Linux64 |
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | |
| DOUBLE-CONVERSION | double-conversion/3.3.0 double-conversion/3.2.1 double-conversion/3.2.0 double-conversion/3.1.5 double-conversion/3.1.4 |
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. | |
| DOXYGEN | 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/1.8.20 Doxygen/1.8.17 Doxygen/1.8.16 Doxygen/1.8.14 |
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. | |
| DRACO | Draco/1.5.6 |
Draco is a library for compressing and decompressing 3D geometric meshes and point clouds. It is intended to improve the storage and transmission of 3D graphics. | |
| 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. | |
| DROP-SEQ | Drop-seq/3.0.2 |
Java and R tools for analyzing Drop-seq data | |
| DS9 | DS9/8.6b1 |
An image display and visualization tool for astronomical data | |
| DSUITE | Dsuite/20240408 |
Fast calculation of the ABBA-BABA statistics across many populations/species | |
| DTCMP | dtcmp/1.1.5 dtcmp/1.1.4 dtcmp/1.1.0 |
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. | |
| DUALSPHYSICS | DualSPHysics/5.0.175-CUDA-11.4.1 |
DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems. | |
| 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. | |
| E3NN | e3nn/0.5.4-CUDA-12.1.1 e3nn/0.3.3-CUDA-12.1.1 |
Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3). | |
| EASYBUILD | EasyBuild/5.1.1 EasyBuild/5.1.0 EasyBuild/5.0.0 EasyBuild/4.9.4 EasyBuild/4.9.2 EasyBuild/4.8.2 EasyBuild/4.7.2 EasyBuild/4.7.1 EasyBuild/4.7.0 EasyBuild/4.6.2 EasyBuild/4.6.0 EasyBuild/4.5.5 EasyBuild/4.5.4 EasyBuild/4.5.1 |
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-FASTER | EasyBuild-faster/0 |
EasyBuild environment variables for building system software in /tmp and installing in /sw/eb on faster.hprc.tamu.edu | |
| EASYBUILD-FASTER-MYEB | EasyBuild-faster-myeb/0 |
User EasyBuild environment for faster.hprc.tamu.edu in $SCRATCH/eb | |
| EASYBUILD-FASTER-SCRATCH | EasyBuild-faster-SCRATCH/0 |
User EasyBuild environment for faster.hprc.tamu.edu in $SCRATCH/eb | |
| EASYBUILD-FASTER-TMP | EasyBuild-faster-tmp/0 |
EasyBuild environment variables for building in /tmp and installing in /sw/eb on faster.hprc.tamu.edu | |
| ECBUILD | ecBuild/3.8.0 ecBuild/3.7.0 |
A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems | |
| ECCODES | ecCodes/2.24.2 ecCodes/2.22.1 |
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). | |
| EDEM | EDEM/2024.1 |
Altair EDEM | |
| EDIRECT | EDirect/23.5.20250218 EDirect/21.5.20240226 EDirect/19.3.20230416-Perl-5.34.1 EDirect/15.2.20210612-Perl-5.30.2 |
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. | |
| EDLIB | edlib/1.3.9 edlib/1.3.8.post1-Python-3.7.4 |
Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. | |
| EDNAFLOW | eDNAFlow/2023.02.06 |
eDNAFlow is a fully automated pipeline that employs a number of state-of-the-art applications to process eDNA data from raw sequences (single-end or paired-end) to generation of curated and non-curated zero-radius operational taxonomic units (ZOTUs) and their abundance tables. | |
| 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/0.3.2-alpha EGAPx/0.3.1-alpha |
EGAPx is the publicly accessible version of the updated NCBI Eukaryotic Genome Annotation Pipeline. | |
| EGGNOG-MAPPER | eggnog-mapper/2.1.11 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/3.3.8 Eigen/3.3.7 Eigen/3.3.4 |
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | |
| EINOPS | einops/0.7.0 einops/0.6.0 einops/0.4.1 einops/0.3.2 |
Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others. | |
| ELFUTILS | elfutils/0.189 elfutils/0.187 elfutils/0.185 elfutils/0.182 |
The elfutils project provides libraries and tools for ELF files and DWARF data. | |
| ELPA | ELPA/2023.11.001 ELPA/2023.05.001 ELPA/2022.05.001CUDA-11.8.0 ELPA/2021.11.001 ELPA/2021.05.001 |
Eigenvalue SoLvers for Petaflop-Applications. | |
| ELSI | ELSI/2.11.0-PEXSI ELSI/2.9.1-PEXSI |
ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems. | |
| EMACS | Emacs/28.2 Emacs/27.2 |
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/6.6.0-Java-13 EMBOSS/6.6.0-Java-11 |
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! | |
| EMIRGE | EMIRGE/0.61.0-Python-2.7.18 |
Expectation-Maximization Iterative Reconstruction of Genes from the Environment | |
| ENCHANT-2 | enchant-2/2.6.5 enchant-2/2.3.3 |
Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant. | |
| ENERGYPLUS | EnergyPlus/23.1.0 EnergyPlus/9.3.0 |
EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption and water use in buildings. | |
| ESM | ESM/2.0.0 |
Evolutionary Scale Modeling | |
| ESMF | ESMF/8.6.0 ESMF/8.3.0 ESMF/8.2.0 ESMF/8.1.1 ESMF/8.0.1 |
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 ETE/3.1.2-Python-3.8.2 |
A Python framework for the analysis and visualization of trees | |
| EVIANN | EviAnn/2.0.1 |
EviAnn -- evidence-based eukaryotic genome annotation software | |
| EVIDENCEMODELER | EVidenceModeler/2.1.0 |
The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. | |
| EXIV2 | exiv2/0.27.5 |
Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. | |
| EXLLSM-CIRCUIT-RECONSTRUCTION | ExLLSM-Circuit-Reconstruction/1.5.0 |
This is a pipeline intended for analyzing expansion lattice light-sheet microscopy (ExLLSM) data, consisting of several independent workflows, and integration with VVD Viewer. | |
| EXO | exo/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| 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/2.6.2 expat/2.5.0 expat/2.4.9 expat/2.4.8 expat/2.4.1 expat/2.2.9 expat/2.2.7 expat/2.2.5 |
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). | |
| EXPECT | expect/5.45.4 |
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications. | |
| 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. | |
| FALCON | FALCON/3.06 |
FALCON is a tool for de novo assembly of long PacBio reads and it is an improved version of its predecessor HGAP. Unlike HGAP, it is a diploid-aware assembler that is better suited to assemble larger genomes. | |
| FASTA | FASTA/36.3.8i |
The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. | |
| FASTAHACK | fastahack/1.0.0 |
Utilities for indexing and sequence extraction from FASTA files. | |
| FASTAINDEX | FastaIndex/0.11c-Python-2.7.18 |
FastA index (.fai) handler compatible with samtools faidx | |
| 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. | |
| FASTCORE | fastcore/1.3.27 |
Adds to Python features inspired by other languages we've loved, like multiple dispatch from Julia, mixins from Ruby, and currying, binding, and more from Haskell. | |
| FASTFILTERS | fastfilters/0.3 |
Fast gaussian and derivative convolutional filters. | |
| FASTME | FastME/2.1.6.3 FastME/2.1.6.1 |
FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. | |
| FASTP | fastp/0.23.4 fastp/0.23.2 fastp/0.20.1 fastp/0.20.0 |
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. | |
| FASTQC | FastQC/0.12.1-Java-11 FastQC/0.11.9-Java-11 FastQC/0.11.8-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. | |
| FASTSIMCOAL2 | fastsimcoal2/2.8.0.0 |
fast sequential Markov coalescent simulation of genomic data under complex evolutionary models | |
| FASTSIMCOAL26 | fastsimcoal26/2.6.0.3 |
fast sequential Markov coalescent simulation of genomic data under complex evolutionary models | |
| 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. | |
| FASTX-TOOLKIT | FASTX-Toolkit/0.0.14 |
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | |
| FDASRSF | fdasrsf/2.3.12 |
A python package for functional data analysis using the square root slope framework and curves using the square root velocity framework which performs pair-wise and group-wise alignment as well as modeling using functional component analysis and regression. | |
| 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/6.0 FFmpeg/5.1.2 FFmpeg/5.0.1 FFmpeg/4.4.2 FFmpeg/4.3.2 FFmpeg/4.3.1 FFmpeg/4.2.2 FFmpeg/4.2.1 |
A complete, cross-platform solution to record, convert and stream audio and video. | |
| FFNVCODEC | 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. | |
| FIGTREE | FigTree/1.4.4-Java-1.8.0 |
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures | |
| FIJI | Fiji/2.15.1 Fiji/2.9.0 |
Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. | |
| FILE | file/5.43 file/5.41 file/5.39 file/5.38 |
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. | |
| FILTLONG | Filtlong/0.2.1 |
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter | |
| FINDBIN | FindBin/1.53 |
Locates the full path to the script bin directory to allow the use of paths relative to the bin directory. | |
| FINESTRUCTURE | fineSTRUCTURE/4.1.1 |
FineSTRUCTURE is software to perform population assignment using large numbers of densely sampled genomes, including both SNP chips and sequence data. | |
| FIONA | Fiona/1.9.5 Fiona/1.8.21 Fiona/1.8.20 Fiona/1.8.16-Python-3.8.2 |
Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely. | |
| FIREFOX | Firefox/118.0.2 Firefox/114.0b9 Firefox/44.0.2 |
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. | |
| FIRESTARTER | FIRESTARTER/2.0 |
FIRESTARTER: A Processor Stress Test Utility. FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by generating heavy load on the execution units as well as transferring data between the cores and multiple levels of the memory hierarchy. | |
| 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/1.3.3 |
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. | |
| FLAKE8 | flake8/6.1.0 flake8/3.9.2 |
Singularity Python (spython) is the Python API for working with Singularity containers. | |
| 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. | |
| FLASH-ATTENTION | flash-attention/2.7.3-CUDA-12.1.1 |
Fast and memory-efficient exact attention. | |
| FLASK | Flask/2.3.3 Flask/2.2.2 Flask/2.0.2 Flask/1.1.2 |
Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors | |
| FLATBUFFERS | flatbuffers/23.5.26 flatbuffers/23.1.4 flatbuffers/2.0.7 flatbuffers/2.0.0 flatbuffers/1.12.0 |
FlatBuffers: Memory Efficient Serialization Library | |
| FLATBUFFERS-PYTHON | flatbuffers-python/23.5.26 flatbuffers-python/23.1.4 flatbuffers-python/2.0 flatbuffers-python/1.12 flatbuffers-python/1.12-Python-3.7.4 |
Python Flatbuffers runtime library. | |
| FLEX | flex/2.6.4 flex/2.6.3 flex/2.6.0 |
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/3.4.4 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. | |
| FLIT | flit/3.9.0 flit/3.2.0 |
A simple packaging tool for simple packages. | |
| FLTK | FLTK/1.3.9 FLTK/1.3.8 FLTK/1.3.7 FLTK/1.3.5 |
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/2.9.4 Flye/2.9.3 Flye/2.9.1 Flye/2.8.3 Flye/2.8.1-Python-3.8.2 |
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. | |
| FMT | fmt/10.2.0 fmt/10.1.0 |
fmt (formerly cppformat) is an open-source formatting library. | |
| FOLDSEEK | Foldseek/2024.07.15-Linux64-avx2 Foldseek/9-427df8a-Linux64-avx2 Foldseek/3-915ef7d-Linux64-avx2 |
Foldseek enables fast and sensitive comparisons of large structure sets. | |
| FONTCONFIG | 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/2.13.92 fontconfig/2.13.1 |
Fontconfig is a library designed to provide system-wide font configuration, customization and application access. | |
| FONTTOOLS | 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/2024.05 foss/2023b foss/2023a foss/2022b foss/2022a foss/2021b foss/2021a foss/2020b foss/2020a foss/2019b foss/2018b |
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | |
| FOSSCUDA | fosscuda/2020b fosscuda/2020a fosscuda/2019b |
GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | |
| FRAGGENESCAN | FragGeneScan/1.31 FragGeneScan/1.30 |
FragGeneScan is an application for finding (fragmented) genes in short reads. | |
| FREEBAYES | FreeBayes/1.3.4-linux-static-AMD64freebayes/1.3.7-R-4.3.2 freebayes/1.3.6-R-4.1.2 |
Bayesian haplotype-based genetic polymorphism discovery and genotyping. | |
| FREEGLUT | freeglut/3.4.0 freeglut/3.2.2 freeglut/3.2.1 |
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. | |
| FREESURFER | FreeSurfer/6.0.1-centos6_x86_64 |
FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. | |
| FREETYPE | freetype/2.13.2 freetype/2.13.0 freetype/2.12.1 freetype/2.11.0 freetype/2.10.4 freetype/2.10.3 freetype/2.10.1 |
FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. | |
| FREEXL | FreeXL/1.0.6 |
FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. | |
| FRIBIDI | FriBidi/1.0.15 FriBidi/1.0.13 FriBidi/1.0.12 FriBidi/1.0.10 FriBidi/1.0.9 FriBidi/1.0.5 |
The Free Implementation of the Unicode Bidirectional Algorithm. | |
| FSA | FSA/1.15.9 |
FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences. | |
| FSL | FSL/6.0.5-slurm |
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | |
| FSOM | fsom/20151117 fsom/20141119 |
A tiny C library for managing SOM (Self-Organizing Maps) neural networks. | |
| FUTHARK | futhark/0.19.5 |
Futhark is a small programming language designed to be compiled to efficient parallel code. It is a statically typed, data-parallel, and purely functional array language in the ML family, and comes with a heavily optimising ahead-of-time compiler that presently generates GPU code via CUDA and OpenCL, although the language itself is hardware-agnostic and can also run on multicore CPUs | |
| G2CLIB | g2clib/1.6.3 g2clib/1.6.0 |
Library contains GRIB2 encoder/decoder ('C' version). | |
| G2LIB | g2lib/3.2.0 g2lib/3.1.0 |
Library contains GRIB2 encoder/decoder and search/indexing routines. | |
| GAPCLOSER | GapCloser/1.12-r6 |
GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads. | |
| GAPPA | gappa/0.8.0 |
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. | |
| GARCON | garcon/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| GATK | GATK/4.5.0.0-Java-17 GATK/4.3.0.0-Java-11 GATK/4.2.6.1-Java-11 GATK/4.2.5.0-Java-11 GATK/4.2.0.0-Java-11 GATK/4.2.0.0-Java-1.8 |
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 |
| GAWK | gawk/5.1.1 gawk/5.0.1 |
The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. | |
| GC | gc/8.2.4 gc/8.2.0 gc/7.6.12 |
The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. | |
| GCATOOLS | GCATools/1.0 |
GCATools is a collection of useful scripts for bioinformatics tasks. | |
| GCC | GCC/13.3.0 GCC/13.2.0 GCC/13.1.0 GCC/12.3.0 GCC/12.2.0 GCC/12.1.0 GCC/11.3.0 GCC/11.2.0 GCC/10.3.0 GCC/10.2.0 GCC/9.3.0 GCC/8.3.0 GCC/7.3.0-2.30 |
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/14.2.0 GCCcore/13.3.0 GCCcore/13.2.0 GCCcore/13.1.0 GCCcore/12.3.0 GCCcore/12.2.0 GCCcore/12.1.0 GCCcore/11.3.0 GCCcore/11.2.0 GCCcore/10.3.0 GCCcore/10.2.0 GCCcore/9.3.0 GCCcore/9.2.0 GCCcore/8.3.0 GCCcore/8.2.0 GCCcore/7.3.0 |
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,...). | |
| GCCCUDA | gcccuda/2020b gcccuda/2020a gcccuda/2019b |
GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. | |
| GCLOUD | gcloud/382.0.0 |
Libraries and tools for interacting with Google Cloud products and services. | |
| GCONF | GConf/3.2.6 |
GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. | |
| 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/2.71 |
GD.pm - Interface to Gd Graphics Library | |
| GDAL | GDAL/3.9.0 GDAL/3.7.1 GDAL/3.6.2 GDAL/3.5.0 GDAL/3.3.2 GDAL/3.3.0 GDAL/3.2.1 GDAL/3.0.4-Python-3.8.2 |
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/13.2 GDB/12.1 |
The GNU Project Debugger | |
| GDBM | gdbm/1.18.1 |
GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database. | |
| GDK-PIXBUF | Gdk-Pixbuf/2.42.10 Gdk-Pixbuf/2.42.8 Gdk-Pixbuf/2.42.6 Gdk-Pixbuf/2.42.0 Gdk-Pixbuf/2.40.0 Gdk-Pixbuf/2.38.2 |
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 gdown/4.7.1-Python-3.8.2 |
Google Drive Public File Downloader when curl/wget Fails | |
| GDRCOPY | GDRCopy/2.4.1 GDRCopy/2.4 GDRCopy/2.3.1 GDRCopy/2.3 GDRCopy/2.2 GDRCopy/2.1-CUDA-11.1.1 GDRCopy/2.1-CUDA-11.0.2 |
A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. | |
| GEANT4 | Geant4/11.0.0 |
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. | |
| GEM | GEM/3.4-Java-1.7.0 |
GEM is a scientific software for studying protein-DNA interaction at high resolution using ChIP-seq/ChIP-exo data. It can also be applied to CLIP-seq and Branch-seq data. | |
| GEMMA | GEMMA/0.98.5 |
Genome-wide Efficient Mixed Model Association | |
| GENEMARK-ET | GeneMark-ET/4.71 GeneMark-ET/4.69 GeneMark-ET/4.68 |
Eukaryotic gene prediction suite with automatic training | |
| 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. | |
| GENOMEALIGNMENTTOOLS | GenomeAlignmentTools/1.0 |
This repository provides tools for improving the sensitivity and specificity of pairwise genome alignments | |
| 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 GenomeTools/1.6.1 |
A comprehensive software library for efficient processing of structured genome annotations. | |
| GEOCUBE | geocube/0.0.14-Python-3.8.2 |
Tool to convert geopandas vector data into rasterized xarray data. | |
| GEOPANDAS | geopandas/0.8.1-Python-3.8.2 |
GeoPandas is a project to add support for geographic data to pandas objects. It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and perform geometric operations. | |
| GEOS | GEOS/3.12.1 GEOS/3.12.0 GEOS/3.11.1 GEOS/3.10.3 GEOS/3.9.1 GEOS/3.8.1-Python-3.8.2 |
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) | |
| GETDIST | GetDist/1.4 |
GetDist is a Python package for analysing Monte Carlo samples, including correlated samples from Markov Chain Monte Carlo (MCMC). | |
| GETTEXT | gettext/0.22.5 gettext/0.22 gettext/0.21.1 gettext/0.21 gettext/0.20.1 gettext/0.19.8.1 |
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/2024.05 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. | |
| GFFCOMPARE | GffCompare/0.12.6 |
GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. | |
| GFFREAD | gffread/0.12.7 gffread/0.11.6 |
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/2.14.3 |
gh is GitHub on the command line. | |
| GHOSTSCRIPT | Ghostscript/10.02.1 Ghostscript/10.01.2 Ghostscript/10.0.0 Ghostscript/9.56.1 Ghostscript/9.54.0 Ghostscript/9.53.3 Ghostscript/9.52 Ghostscript/9.50 |
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/5.2.1 |
giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented. | |
| GIT | git/2.45.1 git/2.42.0 git/2.41.0-nodocs git/2.38.1-nodocs git/2.36.0-nodocs git/2.33.1-nodocs git/2.32.0-nodocs git/2.28.0-nodocs git/2.23.0-nodocs |
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. | |
| GIT-LFS | git-lfs/3.5.1 git-lfs/3.4.0 git-lfs/3.2.0 git-lfs/2.11.0 |
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/3.1.42 GitPython/3.1.40 GitPython/3.1.31 GitPython/3.1.27 GitPython/3.1.24 GitPython/3.1.14 GitPython/3.1.9-Python-3.8.2 GitPython/3.1.0-Python-3.7.4 |
GitPython is a python library used to interact with Git repositories | |
| GKLIB-METIS | GKlib-METIS/5.1.1 |
A library of various helper routines and frameworks used by many of the lab's software | |
| 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 glew/2.1.0 |
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. | |
| GLFW | GLFW/3.3.8 GLFW/3.3.4 |
GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop | |
| GLIB | GLib/2.81.0 GLib/2.80.4 GLib/2.78.1 GLib/2.77.1 GLib/2.75.0 GLib/2.72.1 GLib/2.69.1 GLib/2.68.2 GLib/2.66.1 GLib/2.64.1 GLib/2.62.0 |
GLib is one of the base libraries of the GTK+ project | |
| GLIB-NETWORKING | glib-networking/2.72.1 |
Network extensions for GLib | |
| GLIBC | glibc/2.32 |
The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel. | |
| GLIBMM | GLibmm/2.66.4 GLibmm/2.49.7 |
C++ bindings for Glib | |
| GLIMMERHMM | GlimmerHMM/3.0.4c |
GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models. | |
| GLM | GLM/0.9.9.8 |
OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. | |
| GLOBALARRAYS | GlobalArrays/5.8.2 GlobalArrays/5.8 |
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model | |
| GLOBUS-CLI | Globus-CLI/3.30.1 Globus-CLI/3.6.0 |
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 glog/0.4.0 |
A C++ implementation of the Google logging module. | |
| GLPK | GLPK/5.0 GLPK/4.65 |
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. | |
| GMAP-GSNAP | GMAP-GSNAP/2023-04-20 GMAP-GSNAP/2023-02-17 GMAP-GSNAP/2021-12-17 GMAP-GSNAP/2020-12-17 GMAP-GSNAP/2019-09-12 |
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program | |
| GMPICH | gmpich/2024.06 |
gcc and GFortran based compiler toolchain, including MPICH for MPI support. | |
| GMPY2 | gmpy2/2.1.5 gmpy2/2.1.2 gmpy2/2.1.0b5 gmpy2/2.1.0b4 |
GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x | |
| GNUPG-BUNDLE | gnupg-bundle/20240306 |
GnuPG — The Universal Crypto Engine | |
| GNUPLOT | gnuplot/6.0.1 gnuplot/5.4.8 gnuplot/5.4.6 gnuplot/5.4.4 gnuplot/5.4.2 gnuplot/5.4.1 gnuplot/5.2.8 |
Portable interactive, function plotting utility | |
| GNUTLS | GnuTLS/3.7.8 GnuTLS/3.7.3 |
GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. | |
| GO | Go/1.22.1 Go/1.21.2 Go/1.20.5 Go/1.19.1 Go/1.18.3 Go/1.17.6 Go/1.14.1 |
Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. | |
| GOBFF | gobff/2021a gobff/2020b |
GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW. | |
| GOBJECT-INTROSPECTION | 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/1.66.1 GObject-Introspection/1.64.0-Python-3.8.2 GObject-Introspection/1.63.1-Python-3.7.4 |
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. | |
| GOMKL | gomkl/2023a |
GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL | |
| GOMPI | gompi/2024.05 gompi/2024a gompi/2023b gompi/2023a gompi/2022.05 gompi/2022b gompi/2022a gompi/2021b gompi/2021a gompi/2020b gompi/2020a gompi/2019b gompi/2018b |
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | |
| GOMPIC | gompic/2020b gompic/2020a gompic/2019b |
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. | |
| GOOGLETEST | googletest/1.14.0 googletest/1.13.0 googletest/1.12.1 googletest/1.11.0 googletest/1.10.0 |
Google's framework for writing C++ tests on a variety of platforms | |
| GPAW | GPAW/24.1.0 |
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/3.1 |
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/2.14 gperftools/2.13 gperftools/2.12 gperftools/2.10 gperftools/2.9.1 gperftools/2.7.90 |
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. | |
| GPFLOW | GPflow/2.9.0-CUDA-11.7.0-TensorFlow-2.11.0 |
GPflow is a package for building Gaussian process models in python, using TensorFlow. | |
| GPUSTAT | gpustat/1.1 gpustat/1.0.0b1 gpustat/0.6.0 |
A simple command-line utility for querying and monitoring GPU status | |
| GPY | GPy/1.10.0 |
GPy is a Gaussian Process (GP) framework written in Python | |
| GPYTORCH | GPyTorch/1.6.0 |
GPyTorch is a Gaussian process library implemented using PyTorch. | |
| GRAALVM | GraalVM/22.2.0 GraalVM/21.3.0 |
GraalVM is a high-performance JDK distribution designed to accelerate the execution of applications written in Java and other JVM languages along with support for JavaScript, Ruby, Python, and a number of other popular languages. whatis([==[Homepage: https://www.graalvm.org/ | |
| GRADLE | Gradle/6.9.1 |
Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. | |
| GRAPHENE | Graphene/1.10.8 |
Graphene is a thin layer of types for graphic libraries | |
| GRAPHICSMAGICK | GraphicsMagick/1.3.36 |
GraphicsMagick is the swiss army knife of image processing. | |
| 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/2.50.0 Graphviz/2.47.2 Graphviz/2.47.0-Java-11 Graphviz/2.44.1-Java-11 Graphviz/2.42.2 Graphviz/2.42.2-Python-3.7.4 |
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. | |
| GRAPHVIZ-PYTHON | graphviz-python/0.20.1 |
Simple Python interface for Graphviz | |
| GRASS | GRASS/8.2.0 |
The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization | |
| GREENLET | Greenlet/3.0.3 |
The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. | |
| 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/2023.3-CUDA-11.8.0 GROMACS/2023.1-CUDA-11.7.0 GROMACS/2021.5-PLUMED-2.8.0 GROMACS/2021.5-CUDA-11.4.1 GROMACS/2021.5-CUDA-11.4.1-PLUMED-2.8.0 GROMACS/2021.3 GROMACS/2021 GROMACS/2021-constantph-2022.05.25 GROMACS/2020.5-RAMD-2.0 |
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/1.44.0 |
gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems. | |
| GRPCIO | grpcio/1.57.0 |
gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems. | |
| GSD-VMD | gsd-vmd/v0.4.0 |
HOOMD-blue GSD plugin for VMD | |
| GSLIB | gslib/1.0.8 |
A sparse communication library. | |
| 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 GST-plugins-base/1.18.5 GST-plugins-base/1.18.4 GST-plugins-base/1.16.2 |
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/1.18.5 GStreamer/1.18.4 GStreamer/1.16.2 |
GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. | |
| GTDB-TK | GTDB-Tk/2.3.2 GTDB-Tk/1.7.0-Python-3.8.2 |
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. | |
| GTK+ | GTK+/3.24.23 GTK+/3.24.17 GTK+/3.24.13 |
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. | |
| GTK2 | GTK2/2.24.33 |
The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. | |
| GTK3 | GTK3/3.24.39 GTK3/3.24.37 GTK3/3.24.35 GTK3/3.24.33 GTK3/3.24.31 GTK3/3.24.29 |
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 GTK4/4.7.0 |
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. | |
| GTS | GTS/0.7.6 |
GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. | |
| GUILE | Guile/3.0.9 Guile/3.0.7 Guile/1.8.8 |
Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. | |
| GUROBI | Gurobi/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. | |
| GYMNASIUM | Gymnasium/0.26.3 |
Gymnasium is a standard API for reinforcement learning, and a diverse collection of reference environments. | |
| 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/3.11.0 h5py/3.9.0 h5py/3.8.0 h5py/3.7.0 h5py/3.6.0 h5py/3.2.1 h5py/3.1.0 h5py/2.10.0-Python-3.8.2 h5py/2.10.0-Python-3.7.4 |
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. | |
| HADOOP | Hadoop/2.10.0-native |
Hadoop MapReduce by Cloudera | |
| HAPHIC | HapHiC/2025.01.24 |
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data | |
| HARFBUZZ | HarfBuzz/8.2.2 HarfBuzz/5.3.1 HarfBuzz/4.2.1 HarfBuzz/2.8.2 HarfBuzz/2.8.1 HarfBuzz/2.6.7 HarfBuzz/2.6.4 |
HarfBuzz is an OpenType text shaping engine. | |
| HARVEST-TOOLS | harvest-tools/1.3 |
HarvestTools is a utility for creating and interfacing with Gingr files, which are efficient archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. Though designed for use with Parsnp and Gingr, HarvestTools can also be used for generic conversion between standard bioinformatics file formats. | |
| 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/1.24.2 hatchling/1.18.0 hatchling/1.11.1 |
Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager. | |
| HDBSCAN | HDBSCAN/0.8.38.post1 HDBSCAN/0.8.27 |
The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library provides a high performance implementation of this algorithm, along with tools for analysing the resulting clustering. | |
| HDF | HDF/4.2.16-2 HDF/4.2.15 HDF/4.2.14 |
HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. | |
| HDF5 | HDF5/1.14.3 HDF5/1.14.0 HDF5/1.13.1 HDF5/1.12.2 HDF5/1.12.1 HDF5/1.12.0 HDF5/1.10.8 HDF5/1.10.7 HDF5/1.10.6 HDF5/1.10.5 HDF5/1.10.2 |
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/1.47.10 help2man/1.47.8 help2man/1.47.7 help2man/1.47.4 |
help2man produces simple manual pages from the '--help' and '--version' output of other commands. | |
| HERRO | HERRO/2024.08.01-scripts |
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 | |
| HH-SUITE | HH-suite/3.3.0-2022.05.17 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). | |
| HIC-PRO | HiC-Pro/3.1.0-R-4.2.1 |
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. | |
| HICEXPLORER | HiCExplorer/3.7.2 |
HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization. | |
| HICMATRIX | HiCMatrix/17 |
This library implements the central class of HiCExplorer to manage Hi-C interaction matrices. | |
| HIFIASM | hifiasm/0.24.0 hifiasm/0.23.0 hifiasm/0.21.0 hifiasm/0.20.0 hifiasm/0.19.9-r616 hifiasm/0.19.7 hifiasm/0.19.4-r575 hifiasm/0.16.0 hifiasm/0.15.1 |
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/1.0.7 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'. | |
| HIPIFY-CLANG | hipify-clang/4.2.0 |
Hipify-clang is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced. | |
| HIPSYCL | hipSYCL/0.9.3 |
hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP | |
| 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/3.3.2 HMMER/3.3.1 HMMER/3.2.1 HMMER/3.1b2 |
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. | |
| HMMER2 | HMMER2/2.3.2 |
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. | |
| HOROVOD | Horovod/0.28.1-CUDA-11.7.0-TensorFlow-2.11.0 Horovod/0.23.0-TensorFlow-2.5.0 Horovod/0.22.1-CUDA-11.3.1-TensorFlow-2.6.0 Horovod/0.22.0-PyTorch-1.8.1 Horovod/0.18.2-TensorFlow-1.15.2-Python-3.7.4 |
Horovod is a distributed training framework for TensorFlow. | |
| HPL | HPL/2.3 |
HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. | |
| HPRC_UTILS | HPRC_utils/1.0 |
HPRC_utils is a collection of useful utilities to accompany software modules on the TAMU HPRC clusters. | |
| HTOP | htop/3.0.5 htop/2.0.1 htop/2.0.0 |
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. | |
| HTSEQ | HTSeq/2.0.2 HTSeq/2.0.1 HTSeq/0.11.3 |
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. | |
| HTSLIB | HTSlib/1.20 HTSlib/1.19.1 HTSlib/1.18 HTSlib/1.17 HTSlib/1.15.1 HTSlib/1.14 HTSlib/1.12 HTSlib/1.11 HTSlib/1.10.2 HTSlib/1.9 |
A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix | |
| HUMANN | humann/3.6 |
HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question: What are the microbes in my community-of-interest doing (or capable of doing)? | |
| HWLOC | 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 hwloc/1.11.12 hwloc/1.11.10 |
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. | |
| HYDRA | Hydra/1.3.2 |
Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads. | |
| HYPEROPT | Hyperopt/0.2.7 |
hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions. | |
| HYPHEN | hyphen/20230104 |
Hyphenation library to use converted TeX hyphenation patterns. | |
| HYPHY | HyPhy/2.5.63 |
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/6.103.1 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/5.41.5 hypothesis/5.41.2 hypothesis/4.57.1-Python-2.7.18 hypothesis/4.44.2-Python-3.7.4 |
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/2.31.0 Hypre/2.29.0 Hypre/2.25.0 Hypre/2.24.0 Hypre/2.21.0 Hypre/2.20.0 Hypre/2.18.2 |
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. | |
| ICCIFORT | iccifort/2020.4.304 iccifort/2020.1.217 iccifort/2020.0.166 iccifort/2019.5.281 iccifort/2019.4.243 |
Intel C, C++ & Fortran compilers | |
| ICCIFORTCUDA | iccifortcuda/2020b |
Intel C, C++ & Fortran compilers with CUDA toolkit | |
| ICED | iced/0.5.10 |
Implements the ICE normalization of hic data. | |
| ICU | ICU/75.1 ICU/74.1 ICU/73.2 ICU/72.1 ICU/71.1 ICU/69.1 ICU/67.1 ICU/66.1 ICU/64.2 |
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/1.1.3-maxlen300 |
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/2.17.4-Java-17 IGV/2.16.0-Java-11 IGV/2.9.4-Java-11 |
This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. | HPRC Docs |
| IIMKL | iimkl/2022b |
Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL). | |
| IIMPI | iimpi/2024a iimpi/2023b iimpi/2023a iimpi/2022.12 iimpi/2022.09 iimpi/2022.05 iimpi/2022.00 iimpi/2022b iimpi/2022a iimpi/2021b iimpi/2021a iimpi/2020.12 iimpi/2020b iimpi/2020a iimpi/2019b |
Intel C/C++ and Fortran compilers, alongside Intel MPI. | |
| IIMPIC | iimpic/2020b |
Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA. | |
| IMAGEIO | imageio/2.33.1 imageio/2.31.1 imageio/2.22.2 imageio/2.13.5 imageio/2.9.0 |
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. | |
| IMAGEJ | ImageJ/1.54b-Java-1.8 ImageJ/1.53r-Java-1.8 |
Image Processing and Analysis in Java | |
| IMAGEMAGICK | ImageMagick/7.1.1-34 ImageMagick/7.1.1-15 ImageMagick/7.1.0-53 ImageMagick/7.1.0-37 ImageMagick/7.1.0-4 ImageMagick/7.0.11-14 ImageMagick/7.0.10-35 ImageMagick/7.0.10-1 ImageMagick/7.0.9-5 |
ImageMagick is a software suite to create, edit, compose, or convert bitmap images | |
| IMATH | 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/2023.0.0 imkl/2022.2.1 imkl/2022.2.0 imkl/2022.1.0 imkl/2022.0.1 imkl/2021.4.0 imkl/2021.3.0 imkl/2021.2.0 imkl/2021.1.1 imkl/2020.4.304 imkl/2020.1.217 imkl/2019.5.281 |
Intel oneAPI Math Kernel Library | |
| IMKL-FFTW | imkl-FFTW/2023.2.0 imkl-FFTW/2023.1.0 imkl-FFTW/2023.0.0 imkl-FFTW/2022.2.1 imkl-FFTW/2022.2.0 imkl-FFTW/2022.1.0 imkl-FFTW/2022.0.1 imkl-FFTW/2021.4.0 |
FFTW interfaces using Intel oneAPI Math Kernel Library | |
| IMPI | impi/2021.13.0 impi/2021.11.0 impi/2021.10.0 impi/2021.9.0 impi/2021.8.0 impi/2021.7.1 impi/2021.7.0 impi/2021.6.0 impi/2021.5.0 impi/2021.4.0 impi/2021.3.0 impi/2021.2.0 impi/2021.1.1 impi/2019.9.304 impi/2019.7.217 impi/2018.5.288 |
Intel MPI Library, compatible with MPICH ABI | |
| INFERCNV | InferCNV/1.22.0 |
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/1.1.4 |
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. | |
| INPUTPROTO | inputproto/2.3.1 |
X.org InputProto protocol headers. | |
| INQ | INQ/20230821 |
Library for TDDFT numerical simulations on HPC and GPUs. | |
| INTEL | intel/2023b intel/2022.12 intel/2022.09 intel/2022.05 intel/2022.00 intel/2022b intel/2022a intel/2021b intel/2021a intel/2020.12 intel/2020b intel/2020a intel/2019b intel/Toolkits |
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/2023.0.0 intel-compilers/2022.2.1 intel-compilers/2022.2.0 intel-compilers/2022.1.0 intel-compilers/2022.0.2 intel-compilers/2022.0.1 intel-compilers/2021.4.0 intel-compilers/2021.3.0 intel-compilers/2021.2.0 intel-compilers/2021.1.2 |
Intel C, C++ & Fortran compilers (classic and oneAPI) | |
| INTEL-PYTHON | intel-python/2022.1.0 |
Intel Python distribution. | |
| INTELCUDA | intelcuda/2020b |
Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit | |
| INTERPROSCAN | InterProScan/5.73-104.0 InterProScan/5.72-103.0 InterProScan/5.60-92.0 InterProScan/5.52-86.0 |
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. | |
| IOMKL | iomkl/2022.00 iomkl/2021a |
Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). | |
| IOMPI | iompi/2022.00 iompi/2021a iompi/2020b |
Intel C/C++ and Fortran compilers, alongside Open MPI. | |
| IPYTHON | IPython/8.17.2 IPython/8.14.0 IPython/8.14.0-Python-3.10.8-notebook-6.5.5 IPython/8.5.0 IPython/7.26.0 IPython/7.25.0 IPython/7.18.1 IPython/7.15.0-Python-3.8.2 |
IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. | |
| IQ-TREE | IQ-TREE/2.3.6 IQ-TREE/2.3.5 IQ-TREE/2.2.2.3 IQ-TREE/2.2.1 |
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. | |
| ITK | ITK/5.2.1 |
Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. | |
| JACKIE2 | JACKIE2/2022.07.24 |
JACKIE allows enumeration of all kmer (e.g., SpCas9 binding sites, ZFPs) in a genome and output their sequences, copy numbers and locations. | |
| JAGS | JAGS/4.3.0 |
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/2.13.1 |
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/4.0.0 JasPer/2.0.33 JasPer/2.0.28 JasPer/2.0.24 JasPer/2.0.14 JasPer/1.900.1 |
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/17.0.2 Java/15.0.1 Java/13.0.2 Java/11.0.27 Java/11.0.2 Java/8.452 Java/1.9.0.4 Java/1.8.0_292-OpenJDK Java/1.8.0_281 Java/1.7.0_80 |
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. | |
| JAX | jax/0.4.25-CUDA-12.1.1 jax/0.3.25-CUDA-11.7.0 jax/0.3.23-CUDA-11.7.0 jax/0.3.9 jax/0.3.9-CUDA-11.3.1 jax/0.2.24 jax/0.2.24-CUDA-11.3.1 jax/0.2.19 |
Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more | |
| 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/1.16.11-Perl-5.32.0 |
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 |
| JDFTX | JDFTx/1.7.0 JDFTx/1.7.0-CUDA-12.2.0 |
JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. | |
| JEDI | jedi/0.19.1 jedi/0.19.0 |
Jedi - an awesome autocompletion, static analysis and refactoring library for Python. | |
| 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. | |
| JMOL | Jmol/16.1.59-Java-1.8.0_281 |
Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules | |
| 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/0.15 |
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/9.0.2 |
JSON-Fortran: A Modern Fortran JSON API | |
| JSONCPP | JsonCpp/1.9.5 JsonCpp/1.9.4 JsonCpp/1.9.3 |
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-1.9.0.4-CUDA-8.0.61-CPU |
Juicer is a one-click pipeline for processing terabase scale Hi-C datasets. | |
| JUICER_TOOLS | Juicer_tools/1.22.01-Java-1.9.0.4-CUDA-8.0.61 |
Tools for use with the Juicer application. | |
| JULIA | Julia/1.10.4-linux-x86_64 Julia/1.9.3-linux-x86_64 Julia/1.8.0-linux-x86_64 Julia/1.7.2-linux-x86_64 Julia/1.7.1-linux-x86_64 Julia/1.7.0-linux-x86_64 Julia/1.6.5-linux-x86_64 |
Julia is a high-level, high-performance dynamic programming language for numerical computing | HPRC Docs |
| JUNIT | JUnit/4.12-Java-1.8 |
A programmer-oriented testing framework for Java. | |
| JUPYTER-BUNDLE | Jupyter-bundle/20240522 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/1.0.2 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/4.1.2 jupyter-server-proxy/4.0.0 |
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. | |
| KAHIP | KaHIP/3.16 KaHIP/3.14 |
The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. | |
| KAIJU | Kaiju/1.7.3-Python-3.7.4 |
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/3.3.1 |
Kalign is a fast multiple sequence alignment program for biological sequences. | |
| KALLISTO | kallisto/0.51.1 kallisto/0.48.0 kallisto/0.46.2 |
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | |
| KBPROTO | kbproto/1.0.7 |
X.org KBProto protocol headers. | |
| KENT_TOOLS | Kent_tools/20241218-linux.x86_64 Kent_tools/20211118-linux.x86_64 Kent_tools/468 Kent_tools/460 Kent_tools/442 Kent_tools/411 Kent_tools/401 |
Kent tools: collection of tools used by the UCSC genome browser. | |
| KERAS | Keras/2.4.3 Keras/2.3.1-Python-3.7.4 |
Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. | HPRC Docs |
| KIM-API | kim-api/2.3.0 kim-api/2.2.1 kim-api/2.1.3 |
Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. | |
| KINETO | kineto/0.4.0 |
A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters | |
| KMA | kma/1.4.3 kma/1.3.19 |
KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. | |
| KNITRO | Knitro/13.2 Knitro/12.4 |
The Artelys Knitro Solver is a plug-in Solver Engine that extends Analytic Solver Platform, Risk Solver Platform, Premium Solver Platform or Solver SDK Platform to solve nonlinear optimization problems of virtually unlimited size. | |
| KORFLAB-PERL_UTILS | KorfLab-Perl_utils/2014.05.22 |
Miscellaneous Perl scripts and modules used by people in the Korf lab. | |
| KRAKEN | Kraken/1.1.1 |
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. | |
| KRAKEN2 | Kraken2/2.1.2 |
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 |
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/29Sep2021-kokkos-sm80-noMP LAMMPS/23Jun2022-kokkos LAMMPS/23Jun2022-kokkos-extra-pair-styles LAMMPS/23Jun2022-kokkos-CUDA-11.4.1 LAMMPS/17Nov2016 LAMMPS/3Mar2020-Python-3.8.2-kokkos LAMMPS/3Mar2020-Python-3.7.4-kokkos LAMMPS/2Aug2023_update2-kokkos-CUDA-12.1.1 |
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/3.10.0 LAPACK/3.9.1 |
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. | |
| LASTZ | LASTZ/1.04.22 LASTZ/1.04.03 |
LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. | |
| LATEX | LaTeX/texlive-2021 |
TeX Live is a basic implementation of the TeX typesetting system created by Donald Knuth. The main engine is LaTeX which compiles tex code into printable formats. This build includes some scientific packages for labelling plots. Homepage: https://www.tug.org/texlive/ | |
| LDDT | lDDT/1.2 |
The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure. | |
| LEIDENALG | leidenalg/0.9.1 |
Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python. | |
| LEPTONICA | Leptonica/1.83.0 |
Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. | |
| 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). | |
| LEVELDB | LevelDB/1.22 |
LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. | |
| LEVMAR | levmar/2.6 |
Native ANSI C implementations of the Levenberg-Marquardt optimization algorithm, usable also from C++. Both unconstrained and constrained (under linear equations, inequality and box constraints) Levenberg-Marquardt variants are included. | |
| LFTP | lftp/4.8.4 |
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. | |
| LHSMDU | lhsmdu/1.1 |
A package for generating latin hypercube samples with multi-dimensional uniformity. | |
| LIBAEC | libaec/1.0.6 |
Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. | |
| LIBAIO | libaio/0.3.113 libaio/0.3.112 libaio/0.3.111 |
Asynchronous input/output library that uses the kernels native interface. | |
| LIBARCHIVE | libarchive/3.7.4 libarchive/3.7.2 libarchive/3.6.2 libarchive/3.6.1 libarchive/3.5.1 libarchive/3.4.3 libarchive/3.4.2 |
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/ | |
| LIBBIGWIG | libBigWig/0.4.6 |
A C library for handling bigWig files | |
| LIBCDMS | libcdms/3.1.2-Python-3.8.2 |
Climate Data Management System Library. | |
| LIBCERF | libcerf/2.4 libcerf/2.3 libcerf/2.1 libcerf/1.17 libcerf/1.14 libcerf/1.13 |
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. | |
| LIBCIFPP | libcifpp/3.0.0 |
This library contains code to work with mmCIF and PDB files. | |
| 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/3.20.11 libdap/3.20.8 libdap/3.20.7 libdap/3.20.6 |
A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. | |
| LIBDE265 | libde265/1.0.15 |
libde265 is an open source implementation of the h.265 video codec | |
| LIBDEFLATE | libdeflate/1.20 libdeflate/1.19 libdeflate/1.18 libdeflate/1.15 libdeflate/1.10 libdeflate/1.8 |
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. | |
| LIBDICOM | libdicom/1.11.0 |
C library for reading DICOM files. | |
| LIBDRM | libdrm/2.4.122 libdrm/2.4.117 libdrm/2.4.115 libdrm/2.4.114 libdrm/2.4.110 libdrm/2.4.107 libdrm/2.4.106 libdrm/2.4.102 libdrm/2.4.100 libdrm/2.4.99 |
Direct Rendering Manager runtime library. | |
| LIBDRS | libdrs/3.1.2 |
PCMDI's old DRS format implementation | |
| LIBEPOXY | libepoxy/1.5.10 libepoxy/1.5.8 libepoxy/1.5.4 |
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/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. | |
| LIBFFI | libffi/3.4.5 libffi/3.4.4 libffi/3.4.2 libffi/3.3 libffi/3.2.1 |
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. | |
| LIBFLAME | libFLAME/5.2.0 |
libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK. | |
| LIBFYAML | libfyaml/0.9 |
Fully feature complete YAML parser and emitter, supporting the latest YAML spec and passing the full YAML testsuite. | |
| LIBGCRYPT | libgcrypt/1.10.3 libgcrypt/1.9.3 |
Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG | |
| LIBGD | libgd/2.3.3 libgd/2.3.1 libgd/2.3.0 libgd/2.2.5 |
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/1.7.0 libgeotiff/1.6.0 libgeotiff/1.5.1 |
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 libgit2/1.1.1 libgit2/1.1.0 |
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/1.3.2 libglvnd/1.2.0 |
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. | |
| LIBGPG-ERROR | libgpg-error/1.48 libgpg-error/1.42 |
Libgpg-error is a small library that defines common error values for all GnuPG components. | |
| LIBGPUARRAY | libgpuarray/0.7.6 |
Library to manipulate tensors on the GPU. | |
| LIBHARU | libharu/2.4.4 libharu/2.3.0 |
libHaru is a free, cross platform, open source library for generating PDF files. | |
| LIBHEIF | libheif/1.19.5 |
libheif is an HEIF and AVIF file format decoder and encoder | |
| LIBICONV | libiconv/1.17 libiconv/1.16 libiconv/1.15 |
Libiconv converts from one character encoding to another through Unicode conversion | |
| LIBIDN | libidn/1.41 libidn/1.38 libidn/1.35 |
GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. | |
| LIBIDN2 | libidn2/2.3.7 libidn2/2.3.2 libidn2/2.3.0 |
Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. | |
| LIBINT | Libint/2.7.2-lmax-6-cp2k Libint/2.6.0-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/3.0.1 libjpeg-turbo/2.1.5.1 libjpeg-turbo/2.1.4 libjpeg-turbo/2.1.3 libjpeg-turbo/2.0.6 libjpeg-turbo/2.0.5 libjpeg-turbo/2.0.4 libjpeg-turbo/2.0.3 |
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. | |
| LIBMAD | libmad/0.15.1b |
MAD is a high-quality MPEG audio decoder. | |
| LIBMATHEVAL | libmatheval/1.1.11 |
GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. | |
| LIBMBD | libmbd/0.12.6 libmbd/0.10.4 |
Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. | |
| LIBMESH | Libmesh/1.7.7 Libmesh/1.7.1 |
The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. | |
| LIBNSL | libnsl/2.0.1 libnsl/2.0.0 libnsl/1.3.0 |
The libnsl package contains the public client interface for NIS(YP). | |
| LIBOGG | libogg/1.3.5 libogg/1.3.4 |
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 libpciaccess/0.14 |
Generic PCI access library. | |
| LIBPNG | libpng/1.6.43 libpng/1.6.40 libpng/1.6.39 libpng/1.6.38 libpng/1.6.37 libpng/1.6.34 libpng/1.2.59 |
libpng is the official PNG reference library | |
| LIBPSL | libpsl/0.21.5 libpsl/0.21.1 |
C library for the Public Suffix List | |
| LIBPTHREAD-STUBS | libpthread-stubs/0.4 |
The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. | |
| LIBREADLINE | libreadline/8.2 libreadline/8.1.2 libreadline/8.1 libreadline/8.0 libreadline/7.0 |
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/4.1.2 |
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. | |
| LIBROM | libROM/93ca278 |
A free, lightweight, scalable C++ library for data-driven physical simulation methods from the intrusive projection-based reduced order models to non-intrusive black-box approaches. | |
| LIBROSA | librosa/0.10.1 |
Audio and music processing in Python | |
| LIBRSVG | librsvg/2.55.1 librsvg/2.51.2 |
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. | |
| LIBSAIS | libsais/2.8.5 |
The libsais is a library for fast (see Benchmarks below) linear time suffix array, longest common prefix array and Burrows-Wheeler transform construction based on induced sorting algorithm | |
| LIBSHARP2 | libsharp2/20240830 |
Library for efficient spherical harmonic transforms at arbitrary spins, supporting CPU vectorization, OpenMP and MPI. | |
| LIBSIGC++ | libsigc++/2.10.8 libsigc++/2.10.2 |
The libsigc++ package implements a typesafe callback system for standard C++. | |
| LIBSIGSEGV | libsigsegv/2.12 |
GNU libsigsegv is a library for handling page faults in user mode. | |
| LIBSNDFILE | libsndfile/1.2.2 libsndfile/1.2.0 libsndfile/1.1.0 libsndfile/1.0.31 libsndfile/1.0.28 |
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/3.0.7 |
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. | |
| LIBSPATIALINDEX | libspatialindex/1.9.3 |
C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API | |
| LIBSPATIALITE | libspatialite/5.0.1 |
SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. | |
| LIBSSH | libssh/0.8.9 |
Multiplatform C library implementing the SSHv2 protocol on client and server side | |
| LIBSVM | LIBSVM/3.25 |
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 libtasn1/4.18.0 |
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/4.6.0 LibTIFF/4.5.0 LibTIFF/4.4.0 LibTIFF/4.3.0 LibTIFF/4.2.0 LibTIFF/4.1.0 LibTIFF/4.0.10 |
tiff: Library and tools for reading and writing TIFF data files | |
| LIBTIRPC | libtirpc/1.3.4 libtirpc/1.3.3 libtirpc/1.3.2 libtirpc/1.3.1 libtirpc/1.2.6 |
Libtirpc is a port of Suns Transport-Independent RPC library to Linux. | |
| LIBTOOL | 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/1.1 libunistring/1.0 libunistring/0.9.10 |
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/1.5.0 libunwind/1.4.0 libunwind/1.3.1 |
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 | |
| 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/1.3.2 libwebp/1.3.1 libwebp/1.2.4 libwebp/1.2.0 libwebp/1.1.0 |
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. | |
| LIBWNCK | libwnck/43.0 |
A Window Navigator Construction Kit, i.e. a library to use for writing pagers and taskslists and stuff. | |
| LIBWPE | libwpe/1.16.0 libwpe/1.13.3 |
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. | |
| LIBXAU | libXau/1.0.8 |
The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. | |
| LIBXC | libxc/6.2.2 libxc/6.1.0 libxc/5.2.3 libxc/5.1.6 libxc/5.1.5 libxc/4.3.4 |
Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. | |
| LIBXCB | libxcb/1.11.1 |
The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. | |
| 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. | |
| LIBXFCE4UI | libxfce4ui/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| LIBXFCE4UTIL | libxfce4util/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| LIBXML++ | libxml++/2.42.1 |
libxml++ is a C++ wrapper for the libxml XML parser library. | |
| LIBXML2 | libxml2/2.12.7 libxml2/2.11.5 libxml2/2.11.4 libxml2/2.10.3 libxml2/2.9.13 libxml2/2.9.10 libxml2/2.9.9 libxml2/2.9.8 |
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). | |
| LIBXSLT | 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/1.16.2 |
LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). | |
| LIBYAML | libyaml/0.2.5 libyaml/0.2.2 |
LibYAML is a YAML parser and emitter written in C. | |
| LIBZIP | libzip/1.7.3 |
libzip is a C library for reading, creating, and modifying zip archives. | |
| 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. | |
| LIKWID | likwid/5.2.1 |
Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs. | |
| 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. | |
| LIS | Lis/2.1.7lis/2.0.34 |
Lis (Library of Iterative Solvers for linear systems, pronounced [lis]) is a parallel software library for solving linear equations and eigenvalue problems that arise in the numerical solution of partial differential equations using iterative methods. | |
| LIT | lit/18.1.7 |
lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures. | |
| LITTLECMS | LittleCMS/2.15 LittleCMS/2.14 LittleCMS/2.13.1 LittleCMS/2.12 LittleCMS/2.11 LittleCMS/2.9 |
Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. | |
| LLVM | LLVM/18.1.8 LLVM/16.0.6 LLVM/15.0.5 LLVM/14.0.6 LLVM/14.0.6-llvmlite LLVM/14.0.3 LLVM/13.0.1 LLVM/12.0.1 LLVM/11.1.0 LLVM/11.0.0 LLVM/10.0.1 LLVM/9.0.1 LLVM/9.0.0 LLVM/8.0.1 |
The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. | |
| LMDB | LMDB/0.9.31 LMDB/0.9.29 LMDB/0.9.28 LMDB/0.9.24 |
LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. | |
| 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/1.1.3 |
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. | |
| LOOPY | loopy/2020.2.1 |
Loopy lets you easily generate the tedious, complicated code that is necessary to get good performance out of GPUs and multi-core CPUs. Loopy's core idea is that a computation should be described simply and then transformed into a version that gets high performance.. | |
| 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/ | |
| LSD2 | LSD2/2.4.1 LSD2/2.3 LSD2/1.9.7 |
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/5.4.6 Lua/5.4.4 Lua/5.4.3 Lua/5.4.2 Lua/5.3.5 Lua/5.1.5 |
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. | |
| LUMPY | LUMPY/0.3.1-Python-2.7.16 |
A probabilistic framework for structural variant discovery. | |
| LWGRP | lwgrp/1.0.6 lwgrp/1.0.5 lwgrp/1.0.2 |
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/4.9.3 lxml/4.9.2 lxml/4.9.1 lxml/4.6.3 lxml/4.5.2 |
The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. | |
| LZ4 | lz4/1.9.4 lz4/1.9.3 lz4/1.9.2 |
LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. | |
| LZO | LZO/2.10 |
Portable lossless data compression library | |
| M4 | 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. | |
| MACH | MACH/1.0.18 |
MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. | |
| MACS2 | MACS2/2.2.9.1 |
Model Based Analysis for ChIP-Seq data | |
| MAEPARSER | maeparser/1.3.1 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/7.490-with-extensions MAFFT/7.475-with-extensions MAFFT/7.470-with-extensions MAFFT/7.453-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. | |
| MAGECK | MAGeCK/0.5.9.4 |
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated by Wei Li lab from Children's National Medical Center. | |
| MAGIC-BLAST | Magic-BLAST/1.5.0-x64-linux |
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Unlike other BLAST nucleotide search programs, such as BLASTN or Megablast, Magic-BLAST produces spliced alignments and optimizes alignment scores for paired reads. | |
| MAGMA | MAGMA/1.09bmagma/2.7.2-CUDA-12.1.1 magma/2.6.2-CUDA-11.7.0 magma/2.6.2-CUDA-11.4.1 magma/2.6.1-CUDA-11.3.1 magma/2.5.4 |
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. | |
| MAINMAST | MAINMAST/1.0 |
-------------------------------------------------------------------------------------------------------------------------- MAINMAST: MAINMAST/1.0 -------------------------------------------------------------------------------------------------------------------------- | |
| 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/6.7-minimal |
makeinfo is part of the Texinfo project, the official documentation format of the GNU project. | |
| MAKE_LASTZ_CHAINS | make_lastz_chains/1.0.0 |
Portable Hillerlab solution for generating pairwise genome alignment chains. These chains can be used as input for TOGA or for generating multiz alignments. | |
| MAKO | Mako/1.3.5 Mako/1.2.4 Mako/1.2.0 Mako/1.1.4 Mako/1.1.3 Mako/1.1.2 Mako/1.1.0 |
A super-fast templating language that borrows the best ideas from the existing templating languages | |
| MAMBA | Mamba/23.1.0-4 Mamba/4.14.0-0 |
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. | |
| MARIADB | MariaDB/11.6.0 MariaDB/10.11.8 MariaDB/10.11.6 MariaDB/10.11.2 MariaDB/10.9.3 MariaDB/10.6.4 MariaDB/10.5.8 MariaDB/10.4.13 |
MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. | |
| MARIADB-CONNECTOR-C | MariaDB-connector-c/3.1.7 |
MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. | |
| MASH | Mash/2.3 Mash/2.2 |
Fast genome and metagenome distance estimation using MinHash | |
| MASHMAP | MashMap/3.1.3 |
MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Unlike traditional mappers, MashMap does not compute exact sequence alignments. | |
| MASURCA | MaSuRCA/4.1.1 MaSuRCA/4.0.5 |
MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). | |
| MATHEMATICA | Mathematica/13.2 |
Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. | |
| MATLAB-ENGINE | MATLAB-Engine/9.13.9-R2022b |
The MATLAB Engine API for Python provides a package to integrate MATLAB functionality directly with a Python application, creating an interface to call functions from your MATLAB installation from Python code. | |
| MATLOCK | Matlock/2018.11.02 |
Matlock is a set of tools designed to work with Hi-C data. Functions include bam filtering, conversion, and clustering. | |
| MATPLOTLIB | matplotlib/3.8.2 matplotlib/3.7.2 matplotlib/3.7.0 matplotlib/3.5.2 matplotlib/3.5.1 matplotlib/3.4.3 matplotlib/3.4.2 matplotlib/3.3.3 matplotlib/3.2.1-Python-3.8.2 matplotlib/3.1.1-Python-3.7.4 matplotlib/2.2.5-Python-2.7.18 |
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. | |
| MATURIN | 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. | |
| MAUVE | Mauve/2015.02.13-linux-x64-Java-1.8 |
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. | |
| MAVEN | Maven/3.8.1 Maven/3.6.3 |
Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. | |
| MAXBIN | MaxBin/2.2.7 |
MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. | |
| MBUFFER | mbuffer/20210328 |
mbuffer is a tool for buffering data streams with a large set of unique features. | |
| MCCORTEX | McCortex/1.0.1 |
McCortex is a multi-sample de novo assembly and variant calling using Linked de bruijn graphs. | |
| 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. | |
| MCOUTBRYK | mcOutbryk/2018.06.10 |
mcOutbryk is a SNP calling pipeline using mccortex | |
| MCSCANX | MCScanX/2024.19.19 |
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. | |
| MDANALYSIS | MDAnalysis/0.20.1-Python-3.7.4 |
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. | |
| MDI | 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/1.1.3-Python-3.7.4 |
medaka is a tool to create a consensus sequence from nanopore sequencing data. | |
| MEF90 | MEF90/20240604 |
A reference implementation of the variational approach to fracture. | |
| MEGA | MEGA/10.1.8 |
MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles. | |
| MEGAHIT | MEGAHIT/1.2.9 MEGAHIT/1.2.9-Python-2.7.18 |
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph | |
| MEGAN | MEGAN/6.24.2-Java-17 |
MEGAN is a comprehensive toolbox for interactively analyzing microbiome data | |
| MESA | Mesa/24.1.3 Mesa/23.1.9 Mesa/23.1.4 Mesa/22.2.4 Mesa/22.2.4-LLVM-14.0.6 Mesa/22.0.3 Mesa/21.1.7 Mesa/21.1.1 Mesa/20.2.1 Mesa/20.0.2 Mesa/19.1.7 |
Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. | |
| MESON | Meson/1.4.0 Meson/1.3.1 Meson/1.2.3 Meson/1.1.1 Meson/0.64.0 Meson/0.62.1 Meson/0.59.1-Python-3.7.4 Meson/0.58.2 Meson/0.58.0 Meson/0.55.3 Meson/0.55.1-Python-3.8.2 Meson/0.51.2-Python-3.7.4 |
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. | |
| MESON-PYTHON | meson-python/0.16.0 meson-python/0.15.0 meson-python/0.13.2 meson-python/0.11.0 |
Python build backend (PEP 517) for Meson projects | |
| METABAT | MetaBAT/2.15-Python-2.7.18 |
An efficient tool for accurately reconstructing single genomes from complex microbial communities | |
| METADECODER | MetaDecoder/1.0.19 |
An algorithm for clustering metagenomic sequences | |
| METAEUK | MetaEuk/7 MetaEuk/6 MetaEuk/4 |
MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. | |
| METAPHLAN | MetaPhlAn/4.1.0 MetaPhlAn/4.0.6 MetaPhlAn/3.0.14 MetaPhlAn/3.0.14-Python-3.9.6 |
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data | |
| 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. | |
| MFEM | MFEM/70941b4 MFEM/31bd94e MFEM/4.6 |
MFEM is a modular parallel C++ library for finite element methods. MFEM can be viewed as a finite element toolbox that provides the building blocks for developing finite element algorithms in a manner similar to that of MATLAB for linear algebra methods. | |
| MGLTOOLS | mgltools/1.5.7 |
The MGLTools software suite can be used for visualization and analysis of molecular structures and comprises the Python Molecular Viewer (PMV, a general purpose molecular viewer), AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) and Vision (a visual programming environment). | |
| MICRO-C | Micro-C/2023.08.01 |
Micro-C QC and data analysis | |
| MICROMAMBA | micromamba/2.1.0-0 |
A statically-linked single file version of Mamba. | |
| MINIASM | miniasm/0.3-20191007 |
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. | |
| MINICONDA3 | Miniconda3/23.10.0-1 Miniconda3/23.5.2-0 Miniconda3/23.3.1-0 Miniconda3/22.11.1-1 Miniconda3/4.12.0 Miniconda3/4.9.2 Miniconda3/4.7.10 Miniconda3/4.4.10 |
Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. | |
| 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. | |
| MINIGRAPH | minigraph/0.15 |
Minigraph is a sequence-to-graph mapper and graph constructor. | |
| MINIMAP2 | minimap2/2.28 minimap2/2.26 minimap2/2.24 minimap2/2.23 minimap2/2.22 minimap2/2.20 minimap2/2.18 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. | |
| 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. | |
| MKL-SERVICE | mkl-service/2.3.0 |
Python hooks for Intel(R) Math Kernel Library runtime control settings. | |
| ML-COLLECTIONS | ml-collections/0.1.1 |
ML Collections is a library of Python Collections designed for ML use cases. | |
| MLFLOW | MLflow/2.10.2 |
MLflow is a platform to streamline machine learning development, including tracking experiments, packaging code into reproducible runs, and sharing and deploying models. | |
| MLST | mlst/2.19.0-Perl-5.30.2 |
Scan contig files against traditional PubMLST typing schemes | |
| MLST_CHECK | MLST_Check/2.1.1706216-Perl-5.30.2 |
Multilocus sequence typing by blast using the schemes from PubMLST. | |
| ML_DTYPES | 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/1.0.4 |
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/5.7.2 |
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 MMseqs2/13-45111 |
MMseqs2: ultra fast and sensitive search and clustering suite | |
| MOAB | MOAB/5.5.1 |
The Mesh-Oriented datABase MOAB is a component for representing and evaluating mesh data. | |
| 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. | |
| MOLD | mold/2.4.0 |
mold is a high-performance drop-in replacement for existing Unix linkers. | |
| MOLDEN | Molden/7.3 Molden/7.1 |
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 | |
| MOLMOD | molmod/1.4.5-Python-3.8.2 molmod/1.4.5-Python-3.7.4 |
MolMod is a Python library with many compoments that are useful to write molecular modeling programs. | |
| MOLMODA | MolModa/1.0.1 |
Molecular docking advances early-stage drug discovery by predicting the geometries and affinities of small-molecule compounds bound to drug-target receptors. Researchers can leverage these predictions to prioritize drug candidates for experimental testing. MolModa provides a secure, accessible environment where users can perform molecular docking entirely in their web browsers. | |
| MOOSE | MOOSE/6f5b0e59e8 MOOSE/e70fe56913 |
-------------------------------------------------------------------------------------------------------------------------- MOOSE: MOOSE/6f5b0e59e8 -------------------------------------------------------------------------------------------------------------------------- | HPRC Docs |
| MOTHUR | Mothur/1.48.0 |
Mothur is 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. | |
| MOTIONCOR2 | MotionCor2/1.3.2 |
MotionCor2 correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 | |
| MPC | MPC/1.3.1 MPC/1.2.1 MPC/1.1.0 |
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 MPFR/4.0.2 |
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. | |
| MPI4PY | mpi4py/3.1.5 mpi4py/3.1.4 |
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. | |
| MPICH | MPICH/4.2.1 |
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/0.11.1 mpifileutils/0.10.1 |
MPI-Based File Utilities For Distributed Systems | |
| MPMATH | mpmath/1.1.0-Python-3.8.2 |
mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work. | |
| MRCFILE | mrcfile/1.5.0 mrcfile/1.4.3 |
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. | |
| MSGPACK-C | msgpack-c/3.3.0 |
MessagePack is an efficient binary serialization format, which lets you exchange data among multiple languages like JSON, except that it's faster and smaller. Small integers are encoded into a single byte while typical short strings require only one extra byte in addition to the strings themselves. | |
| MSTORE | mstore/0.3.0 |
Molecular structure store for testing | |
| MUJOCO | MuJoCo/2.2.2 MuJoCo/2.1.1 |
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. | |
| MUJOCO-PY | mujoco-py/2.1.2.14 |
MuJoCo is a physics engine for detailed, efficient rigid body simulations with contacts. mujoco-py allows using MuJoCo from Python 3. | |
| MULTICHARGE | multicharge/0.3.0 |
Electronegativity equilibration model for atomic partial charges. | |
| MULTICHOOSE | multichoose/1.0.3 |
generate multiset combinations (n multichoose k). | |
| MULTIQC | MultiQC/1.27.1 MultiQC/1.22.3 MultiQC/1.14 MultiQC/1.12 MultiQC/1.9-Python-3.8.2 |
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. | |
| MUMMER | MUMmer/4.0.0rc1 MUMmer/4.0.0beta2 MUMmer/3.23 |
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. | |
| MUMPS | MUMPS/5.6.1-metis MUMPS/5.5.1-metis MUMPS/5.4.1-metis MUMPS/5.4.0-metis MUMPS/5.3.5-metis MUMPS/5.2.1-metis |
A parallel sparse direct solver | |
| MUSCLE | MUSCLE/5.1.0 MUSCLE/3.8.1551 MUSCLE/3.8.31 |
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. | |
| MVAPICH2 | MVAPICH2/2.3.6 |
This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. | |
| NAMD | NAMD/2.14 NAMD/2.14-CUDA-11.7.0 |
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | HPRC Docs |
| NAMFINDER | namfinder/0.1.3 |
namfinder: Fast computation of shared regions between sequences | |
| NANOFILT | NanoFilt/2.6.0-Python-3.7.4 |
Filtering and trimming of long read sequencing data. | |
| NANOFLANN | nanoflann/1.5.5 |
nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies. | |
| NANOGET | nanoget/1.19.1 |
Functions to extract information from Oxford Nanopore sequencing data and alignments | |
| NANOMATH | nanomath/1.3.0 |
A few simple math functions for other Oxford Nanopore processing scripts | |
| NAPARI | napari/0.4.18 |
napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy). | |
| NASM | NASM/2.16.03 NASM/2.16.01 NASM/2.15.05 NASM/2.14.02 |
NASM: General-purpose x86 assembler | |
| 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/3.1.1 ncbi-vdb/3.0.10 ncbi-vdb/3.0.2 ncbi-vdb/2.11.2 ncbi-vdb/2.10.9 ncbi-vdb/2.10.7 |
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/2.16.2-CUDA-12.0.0 NCCL/2.12.12-CUDA-11.7.0 NCCL/2.11.4 NCCL/2.11.4-CUDA-11.4.1 NCCL/2.10.3-CUDA-11.4.1 NCCL/2.10.3-CUDA-11.3.1 NCCL/2.8.3-CUDA-11.1.1 NCCL/2.8.3-CUDA-11.0.2 NCCL/2.4.8 |
The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. | |
| NCCL-TESTS | NCCL-tests/2.13.6-CUDA-11.7.0 |
Tests check both the performance and the correctness of NCCL operations. | |
| NCDU | ncdu/1.20 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/5.1.0 NCO/5.0.3 NCO/5.0.1 NCO/4.9.7 NCO/4.9.3 |
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 ncurses/6.0 ncurses/5.9 |
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/2.1.7 |
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/4.6.1 |
Neper is a software package for polycrystal generation and meshing. It can deal with 2D and 3D polycrystals with very large numbers of grains. | |
| NETCDF | netCDF/4.9.2 netCDF/4.9.0 netCDF/4.8.1 netCDF/4.8.0 netCDF/4.7.4 netCDF/4.7.1 netCDF/4.6.1 |
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. | 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/4.9.2-gompi-2023a netCDF-combined/4.9.0 netCDF-combined/4.8.1-gompi-2021b netCDF-combined/4.7.4 |
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-Fortran/4.5.2 netCDF-Fortran/4.4.4 |
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. | |
| NETCDF4-PYTHON | netcdf4-python/1.5.7 netcdf4-python/1.5.3-Python-3.8.2 netcdf4-python/1.5.3-Python-3.7.4 |
Python/numpy interface to netCDF. | |
| NETTLE | nettle/3.9.1 nettle/3.8.1 nettle/3.8 nettle/3.7.3 nettle/3.7.2 nettle/3.6 nettle/3.5.1 |
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. | |
| NEUROMANCER | NeuroMANCER/1.5.3-CUDA-12.1.1 |
"Neural Modules with Adaptive Nonlinear Constraints and Efficient Regularizations (NeuroMANCER) is an open-source differentiable programming (DP) library for solving parametric constrained optimization problems, physics-informed system identification, and parametric model-based optimal control. | |
| NEWICK_UTILS | newick_utils/2.15.05 |
The Newick Utilities are a suite of programs for working with Newick-formatted phylogenetic trees. | |
| NEXTDENOVO | NextDenovo/2.5.0 |
NextDenovo is a string graph-based de novo assembler for TGS long reads. | |
| NEXTFLOW | Nextflow/24.10.3 Nextflow/24.04.2 Nextflow/23.10.0 Nextflow/22.10.6 Nextflow/22.10.6-Java-13 Nextflow/21.08.0 |
Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data | |
| NEXTPOLISH | NextPolish/1.4.1 NextPolish/1.4.1b |
NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. | |
| NGHTTP2 | nghttp2/1.58.0 nghttp2/1.48.0 |
This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API. | |
| NGHTTP3 | nghttp3/1.3.0 nghttp3/0.6.0 |
nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation. | |
| NGS | NGS/2.11.2 NGS/2.10.9 NGS/2.10.5 |
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 ngtcp2/0.7.0 |
'Call it TCP/2. One More Time.' ngtcp2 project is an effort to implement RFC9000 QUIC protocol. | |
| NLOHMANN_JSON | nlohmann_json/3.11.3 nlohmann_json/3.11.2 nlohmann_json/3.10.5 |
JSON for Modern C++ | |
| NLOPT | NLopt/2.7.1 NLopt/2.7.0 NLopt/2.6.2 NLopt/2.6.1 |
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/3.7 NLTK/3.6.7 |
NLTK is a leading platform for building Python programs to work with human language data. | |
| NODEJS | nodejs/20.9.0 nodejs/18.17.1 nodejs/18.12.1 nodejs/16.15.1 nodejs/14.17.6 nodejs/14.17.0 nodejs/12.19.0 nodejs/12.16.1 |
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. | |
| NSEG | nseg/1.0.1 |
nseg identifies and masks regions of low complexity in nucleic acid sequences. | |
| NSPR | NSPR/4.35 NSPR/4.34 NSPR/4.32 NSPR/4.30 NSPR/4.29 NSPR/4.25 NSPR/4.21 |
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. | |
| NSS | NSS/3.94 NSS/3.89.1 NSS/3.85 NSS/3.79 NSS/3.69 NSS/3.65 NSS/3.57 NSS/3.51 NSS/3.45 |
Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. | |
| NSYNC | nsync/1.26.0 nsync/1.25.0 nsync/1.24.0 |
nsync is a C library that exports various synchronization primitives, such as mutexes | |
| NTLINK | ntLink/1.3.11 ntLink/1.3.10 |
Minimizer-based genome assembly scaffolding and mapping using long reads and minimizers | |
| NTPOLY | NTPoly/3.1.0 NTPoly/2.7.1 |
is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time. | |
| NUITKA | Nuitka/0.9.6 |
Nuitka is the optimizing Python compiler written in Python that creates executables that run without an need for a separate installer. | |
| NUMACTL | numactl/2.0.18 numactl/2.0.16 numactl/2.0.14 numactl/2.0.13 numactl/2.0.12 numactl/2.0.11 |
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/0.58.1 numba/0.58.1-CUDA-12.1.1 numba/0.56.4 numba/0.56.4-CUDA-12.2.0 numba/0.56.4-CUDA-11.7.0 numba/0.54.1 numba/0.54.1-CUDA-11.4.1 numba/0.53.1 numba/0.52.0 numba/0.50.0-Python-3.8.2 |
Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code. | |
| NUMEXPR | numexpr/2.7.1-Python-3.9.6 numexpr/2.7.1-Python-3.8.6 numexpr/2.7.1-Python-3.8.2 numexpr/2.7.1-Python-3.7.4 |
The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. | |
| NV-CODEC-HEADERS | nv-codec-headers/11.1.5.2 |
FFmpeg version of headers required to interface with Nvidias codec APIs. | |
| NVBIO | NVBIO/2020.02.05-GCC-8.3.0-CUDA-10.1.243 |
NVBIO is a library of reusable components designed by NVIDIA Corporation to accelerate bioinformatics applications using CUDA. It contains the nvBowtie and nvLighter applications. | |
| NVCOMP | nvCOMP/2.2.0 |
A CUDA library that features generic compression interfaces to enable developers to use high-performance GPU compressors and decompressors in their applications. | |
| NVHPC | NVHPC/24.9-CUDA-12.6.0 NVHPC/24.1-CUDA-12.3.0 NVHPC/23.7-CUDA-12.2.0 NVHPC/22.7-CUDA-11.7.0 NVHPC/21.9 NVHPC/20.7 |
C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) | |
| NVIDIA-CONTAINER-CLI | nvidia-container-cli/1.13.2-1-hprc nvidia-container-cli/1.11.0-hprc |
NVIDIA container command line tools provides a list of locally installed libraries that Charliecloud needs to interface to the local NVIDIA GPUs. | |
| NVSHMEM | NVSHMEM/2.8.0-CUDA-11.7.0 |
NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a global address space for data that spans the memory of multiple GPUs and can be accessed with fine-grained GPU-initiated operations, CPU-initiated operations, and operations on CUDA streams. | |
| NVTOP | nvtop/1.2.1 |
htop-like GPU usage monitor | |
| OBITOOLS3 | OBITools3/3.0.1b8 |
A package for the management of analyses and data in DNA metabarcoding. | |
| OCTAVE | Octave/7.1.0 |
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. | |
| OCTOPUS | octopus/14.1 |
Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. | |
| OCTOPUS-VCF | Octopus-vcf/0.7.4 |
Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time. | |
| OGDF | OGDF/dogwood-202202 |
OGDF is a self-contained C++ library for graph algorithms, in particular for (but not restricted to) automatic graph drawing. It offers sophisticated algorithms and data structures to use within your own applications or scientific projects. | |
| ONEAPI/2022.1.1 | oneAPI/2022.1.1 |
-------------------------------------------------------------------------------------------------------------------------- oneAPI/2022.1.1: oneAPI/2022.1.1 -------------------------------------------------------------------------------------------------------------------------- | |
| ONEAPI/2022.2.0 | oneAPI/2022.2.0 |
-------------------------------------------------------------------------------------------------------------------------- oneAPI/2022.2.0: oneAPI/2022.2.0 -------------------------------------------------------------------------------------------------------------------------- | |
| ONNX | ONNX/1.11.0 |
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). | |
| ONNX-RUNTIME | ONNX-Runtime/1.10.0 ONNX-Runtime/1.10.0-CUDA-11.3.1 |
ONNX Runtime inference can enable faster customer experiences and lower costs, supporting models from deep learning frameworks such as PyTorch and TensorFlow/Keras as well as classical machine learning libraries such as scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different hardware, drivers, and operating systems, and provides optimal performance by leveraging hardware accelerators where applicable alongside graph optimizations and transforms. | |
| ONT-FAST5-API | ont-fast5-api/4.1.2 ont-fast5-api/4.0.2 |
ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. | |
| ONT-GUPPY | ont-guppy/6.4.8-CUDA-11.7.0 |
Guppy is a bioinformatics toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. For Research Use Only | |
| ONT-GUPPY-CPU | ont-guppy-cpu/6.3.8-Linux64 |
Guppy is a neural network based basecaller that in addition to basecalling also performs filtering of low quality reads, clipping of Oxford Nanopore adapters and estimation of methylation probabilities per base. | |
| OPEN-DATA-CUBE-CORE | Open-Data-Cube-Core/1.8.3-Python-3.8.2 |
The Open Data Cube Core provides an integrated gridded data analysis environment for decades of analysis ready earth observation satellite and related data from multiple satellite and other acquisition systems. | |
| OPENAI-GYM | OpenAI-Gym/0.26.2 OpenAI-Gym/0.21.0 |
A toolkit for developing and comparing reinforcement learning algorithms. | |
| OPENBABEL | OpenBabel/3.1.1 OpenBabel/3.1.1-Python-3.7.4 OpenBabel/3.0.0-Python-3.7.4 |
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/0.3.27 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/0.3.12 OpenBLAS/0.3.7 OpenBLAS/0.3.1 |
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | |
| OPENCENSUS-PYTHON | OpenCensus-python/0.8.0 |
OpenCensus for Python. OpenCensus provides a framework to measure a server's resource usage and collect performance stats. This repository contains Python related utilities and supporting software needed by OpenCensus. | |
| OPENCV | OpenCV/4.8.1-CUDA-12.1.1-contrib OpenCV/4.8.0-contrib OpenCV/4.6.0-CUDA-11.7.0-contrib OpenCV/4.5.5-contrib OpenCV/4.5.3-CUDA-11.3.1-contrib OpenCV/4.2.0-Python-3.8.2 |
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/3.2.0 OpenEXR/3.1.7 OpenEXR/3.1.5 OpenEXR/3.1.1 OpenEXR/3.0.1 OpenEXR/2.5.5 |
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/8 OpenFOAM/v2306 OpenFOAM/v2206 OpenFOAM/v2112 OpenFOAM/v2012 OpenFOAM/v2006 |
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/2.5.0 OpenJPEG/2.4.0 |
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. | |
| OPENMC | OpenMC/0.15.0 OpenMC/0.15.0-Libmesh-1.7.7 OpenMC/0.15.0-Libmesh-1.7.1 |
The OpenMC project aims to provide a fully-featured Monte Carlo particle transport code based on modern methods. | |
| OPENMM | OpenMM/8.1.1 OpenMM/8.0.0-CUDA-12.1.1 OpenMM/8.0.0-CUDA-11.7.0 OpenMM/7.7.0 OpenMM/7.5.1-DeepMind-patch OpenMM/7.5.0 OpenMM/7.5.0-Python-3.8.2 |
OpenMM is a toolkit for molecular simulation. | |
| OPENMPI | OpenMPI/5.0.3 OpenMPI/4.1.6 OpenMPI/4.1.5 OpenMPI/4.1.4 OpenMPI/4.1.4-EB OpenMPI/4.1.4-CUDA-11.8.0 OpenMPI/4.1.3 OpenMPI/4.1.2 OpenMPI/4.1.1 OpenMPI/4.0.5 OpenMPI/4.0.3 OpenMPI/3.1.6 OpenMPI/3.1.4 OpenMPI/3.1.1 |
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/3.1.2 |
A Python library to read/write Excel 2010 xlsx/xlsm files | |
| OPENSSL | OpenSSL/3 OpenSSL/1.1.1n OpenSSL/1.1.1k OpenSSL/1.1.1h OpenSSL/1.1.1e OpenSSL/1.1.1d OpenSSL/1.1 |
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. | |
| OPTAX | Optax/0.2.2-CUDA-12.1.1 Optax/0.1.7-CUDA-11.7.0 |
Optax is a gradient processing and optimization library for JAX. | |
| OPTIX | OptiX/7.2.0 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. | |
| OPTUNA | Optuna/2.10.0 Optuna/2.9.1 |
Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning. It features an imperative, define-by-run style user API. Thanks to our define-by-run API, the code written with Optuna enjoys high modularity, and the user of Optuna can dynamically construct the search spaces for the hyperparameters. | |
| ORCA | ORCA/6.0.1-avx2 ORCA/5.0.4 ORCA/5.0.3orca/1.3.0 |
Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line. | |
| ORTHOFINDER | OrthoFinder/2.5.5 |
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics | |
| OSI | Osi/0.108.9 Osi/0.108.8 Osi/0.108.7 |
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. | |
| OSU-MICRO-BENCHMARKS | OSU-Micro-Benchmarks/5.9 OSU-Micro-Benchmarks/5.9-CUDA-11.3.1 OSU-Micro-Benchmarks/5.7.1-CUDA-11.3.1 |
OSU Micro-Benchmarks | |
| P11-KIT | p11-kit/0.25.3 p11-kit/0.24.1 |
Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process. | |
| 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/1.1.0 |
pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. | |
| 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/4.9j |
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | |
| PANDAS | pandas/1.4.0-Python-3.9.6 pandas/1.3.1-Python-3.8.6 pandas/1.1.2-Python-3.8.2 |
pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language. | |
| PANDOC | Pandoc/3.5 |
If you need to convert files from one markup format into another, pandoc is your swiss-army knife | |
| PANGO | Pango/1.51.0 Pango/1.50.14 Pango/1.50.12 Pango/1.50.7 Pango/1.48.8 Pango/1.48.5 Pango/1.47.0 Pango/1.44.7 |
Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. | |
| 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/4.0.1 |
Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generation 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/20210622 parallel/20210322 parallel/20200522 parallel/20190922 |
parallel: Build and execute shell commands in parallel | |
| PARALLEL-HASHMAP | Parallel-Hashmap/1.36 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. | |
| PARALLELFOLD | ParallelFold/2021.12.02 ParallelFold/2021.10.28 ParallelFold/2.0-CUDA-11.7.0 |
This project is a modified version of DeepMind's AlphaFold2 to achieve high-throughput protein structure prediction. | |
| PARAMETERIZED | parameterized/0.9.0 |
Parameterized testing with any Python test framework | |
| PARASAIL | parasail/2.6.2 parasail/2.6 parasail/2.5 parasail/2.4.1 |
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-CUDA-12.1.1 ParaView/5.12.0-MPI-Linux64 ParaView/5.11.1 ParaView/5.11.0-mpi-cuda ParaView/5.10.1-mpi ParaView/5.9.1-mpi ParaView/5.8.1-mpi ParaView/5.8.0-Python-3.8.2-mpi |
ParaView is a scientific parallel visualizer. | |
| PARMED | ParmEd/4.2.2 |
ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python. | |
| 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. | |
| PARSNP | Parsnp/2.1.2 Parsnp/1.2-Linux64 |
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. | |
| PASA | PASA/2.5.2-Perl-5.30.2 |
PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. | |
| PATCHELF | patchelf/0.18.0 patchelf/0.17.2 patchelf/0.15.0 patchelf/0.13 |
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. | |
| PCANGSD | PCAngsd/1.10 |
PCAngsd, which estimates the covariance matrix for low depth NGS data in an iterative procedure based on genotype likelihoods and is able to perform multiple population genetic analyses in heterogeneous populations. | |
| PCRE | PCRE/8.45 PCRE/8.44 PCRE/8.43 |
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. | |
| PCRE2 | PCRE2/10.43 PCRE2/10.42 PCRE2/10.40 PCRE2/10.37 PCRE2/10.36 PCRE2/10.35 PCRE2/10.34 PCRE2/10.33 |
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/2.6.0 PDAL/2.4.3 |
PDAL is a C++ library for translating and manipulating point cloud data. | |
| PDM | PDM/2.12.4 |
A modern Python package and dependency manager supporting the latest PEP standards. | |
| PEPPER | PEPPER/0.8-CUDA-11.3.1 |
PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline. | |
| PERL | 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/5.34.0-minimal Perl/5.32.1 Perl/5.32.1-minimal Perl/5.32.0 Perl/5.32.0-minimal Perl/5.30.2 Perl/5.30.2-minimal Perl/5.30.0 Perl/5.30.0-minimal Perl/5.28.0 |
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/5.38.2 Perl-bundle-CPAN/5.38.0 Perl-bundle-CPAN/5.36.1 |
A set of common packages from CPAN | |
| PERL-BUNDLE1-CPAN | Perl-bundle1-CPAN/5.36.1 |
A set of common packages from CPAN | |
| PETSC | PETSc/3.18.4 PETSc/3.15.1 PETSc/3.14.4 PETSc/3.12.4-Python-3.8.2 PETSc/3.12.4-Python-3.7.4 PETSc/3.6.2-Python-2.7.16 |
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. | |
| PFFT | PFFT/20181230pfft/1.0.8-alpha |
PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. | |
| PFTOOLSV3 | pftoolsV3/3.2.12 pftoolsV3/3.2.11 |
A suite of tools to build and search generalized profiles (protein and DNA). | |
| PGDSPIDER | PGDSpider/2.1.1.5-Java-1.7.0_80 |
An automated data conversion tool for connecting population genetics and genomics programs | |
| PGENOMICS | pgenomics/1.0.1 |
pgenomics is a bundle of software modules for use with plant genomics workflows. | |
| PHAROKKA | pharokka/1.7.4 |
pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. | |
| PHAST | PHAST/1.5 |
PHAST is a freely available software package for comparative and evolutionary genomics. | |
| PHIPACK | PhiPack/2016.06.14 |
The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well. | |
| PHOBIUS | Phobius/1.01 Phobius/1.01-Perl-5.30.2 |
Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. | |
| PHP | php/8.2.0 |
PHP is a popular general-purpose scripting language that is especially suited to web development. | |
| PHYLIP | PHYLIP/3.697 |
PHYLIP is a free package of programs for inferring phylogenies. | |
| PHYLOFLASH | phyloFlash/3.4.2-Python-2.7.18 |
phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset. | |
| PHYLOPHLAN | PhyloPhlAn/3.0.3 |
PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. | |
| PHYML | PHYML/3.3.20220408 |
PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. | |
| PHYSICS-TENPY | physics-tenpy/0.10.0 physics-tenpy/0.10.0-Python-3.10.4 |
TeNPy (short for ‘Tensor Network Python’) is a Python library for the simulation of strongly correlated quantum systems with tensor networks. | |
| PICARD | picard/3.3.0-Java-17 picard/2.25.1-Java-11 picard/2.25.0-Java-11 |
A set of tools (in Java) for working with next generation sequencing data in the BAM format. | |
| PIGZ | pigz/2.8 pigz/2.7 pigz/2.6 pigz/2.4 |
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/9.5.0 Pillow-SIMD/9.2.0 Pillow-SIMD/8.2.0 Pillow-SIMD/7.1.2 Pillow-SIMD/6.0.x.post0 |
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. | |
| PIXMAN | pixman/0.42.2 pixman/0.40.0 pixman/0.38.4 |
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/2.2.0 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. | |
| PKGCONFIG | pkgconfig/1.5.5-python pkgconfig/1.5.4-python pkgconfig/1.5.1-Python-3.8.2 pkgconfig/1.5.1-Python-3.7.4 pkgconfig/1.5.1-python |
pkgconfig is a Python module to interface with the pkg-config command line tool | |
| PLATANUS | Platanus/1.2.4 |
PLATform for Assembling NUcleotide Sequences | |
| PLATYPUS | Platypus/1.1.0 |
Platypus is a framework for evolutionary computing in Python with a focus on multiobjective evolutionary algorithms (MOEAs). | |
| PLINK | PLINK/2.00a3.7 PLINK/2.00a3.1 |
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.PY | plotly.py/5.23.0 plotly.py/5.18.0 plotly.py/5.12.0 plotly.py/5.4.0 plotly.py/5.1.0 plotly.py/4.14.3 plotly.py/4.8.1 |
An open-source, interactive graphing library for Python | |
| PLUMED | PLUMED/2.9.3 PLUMED/2.9.0 PLUMED/2.8.1 PLUMED/2.8.0 PLUMED/2.7.3 PLUMED/2.7.2 PLUMED/2.7.0 PLUMED/2.6.0-Python-3.8.2 PLUMED/2.5.3-Python-3.7.4 |
PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. | |
| PLY | PLY/3.11 |
PLY is yet another implementation of lex and yacc for Python. | |
| PMIX | PMIx/5.0.2 PMIx/4.2.6 PMIx/4.2.4 PMIx/4.2.2 PMIx/4.1.2 PMIx/4.1.1 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/1.12.3 PnetCDF/1.12.2 |
Parallel netCDF: A Parallel I/O Library for NetCDF File Access | |
| POCL | pocl/4.0 pocl/1.8 pocl/1.6 pocl/1.4 |
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/0.1.8 pod5-file-format/0.0.41-Linux64 |
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/1.8.3 poetry/1.7.1 poetry/1.6.1 poetry/1.5.1 poetry/1.2.2 poetry/1.1.6 poetry/1.0.9 poetry/1.0.9-Python-3.8.2 poetry/1.0.9-Python-3.7.4 |
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. | |
| POLARS | 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/23.09.0 poppler/22.12.0 poppler/21.06.1 |
Poppler is a PDF rendering library | |
| POPT | popt/1.16 |
Popt is a C library for parsing command line parameters. | |
| PORECHOP | Porechop/0.2.4 |
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity | |
| POSTGRESQL | PostgreSQL/16.1 PostgreSQL/13.4 PostgreSQL/12.4 |
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 POV-Ray/3.7.0.8 |
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. | |
| PRESEQ | preseq/3.2.0 |
Software for predicting library complexity and genome coverage in high-throughput sequencing. | |
| PROBTORCH | probtorch/0.1.0 |
Probabilistic Torch is library for deep generative models that extends PyTorch. | |
| 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. | |
| PRODY | ProDy/2.4.1 |
ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. | |
| PROJ | PROJ/9.3.1 PROJ/9.2.0 PROJ/9.1.1 PROJ/9.0.0 PROJ/8.1.0 PROJ/8.0.1 PROJ/7.2.1 PROJ/7.0.0 PROJ/6.2.1 |
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. | |
| PROTOBUF | protobuf/27.3-GraphAligner protobuf/25.3 protobuf/24.0 protobuf/23.0 protobuf/3.19.4 protobuf/3.17.3 protobuf/3.14.0 protobuf/3.13.0 protobuf/3.10.0 protobuf/2.5.0 |
Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data. | |
| PROTOBUF-PYTHON | 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 protobuf-python/3.14.0 protobuf-python/3.13.0-Python-3.8.2 protobuf-python/3.10.0-Python-3.7.4 |
Python Protocol Buffers runtime library. | |
| PROTOC | protoc/27.2 |
Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data. | |
| PRRTE | PRRTE/3.0.5 |
PRRTE is the PMIx Reference RunTime Environment | |
| PSCOM | pscom/5.4-default-CUDA-11.5.0 |
ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer. | |
| PSUTIL | psutil/5.9.8 psutil/5.9.5 psutil/5.9.3 psutil/5.8.0 psutil/5.6.3 |
A cross-platform process and system utilities module for Python | |
| PSYCOPG | psycopg/3.1.18 |
Psycopg is the most popular PostgreSQL adapter for the Python programming language. | |
| PSYCOPG2 | psycopg2/2.9.9 psycopg2/2.9.5 psycopg2/2.8.6-Python-3.8.2 |
Psycopg is the most popular PostgreSQL adapter for the Python programming language. | |
| PUGIXML | pugixml/1.15 pugixml/1.14 pugixml/1.12.1 |
pugixml is a light-weight C++ XML processing library | |
| PULLSEQ | pullseq/1.0.2 |
Utility program for extracting sequences from a fasta/fastq file | |
| 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. | |
| PULSEAUDIO | pulseaudio/17.0 |
PulseAudio is a sound server system for POSIX OSes, meaning that it is a proxy for your sound applications. It is an integral part of all relevant modern Linux distributions and is used in various mobile devices, by multiple vendors. It performs advanced operations on sound data as it passes between your application and hardware. Things like transferring audio to a different machine, changing the sample format or channel count, or mixing several sounds into one input/output, are easily achieved using PulseAudio. | |
| 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/0.10.0 pybedtools/0.9.1 pybedtools/0.9.0 pybedtools/0.8.2 |
pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. | |
| PYBIGWIG | pyBigWig/0.3.18 pyBigWig/0.3.17 |
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 pybind11/2.7.1 pybind11/2.7.1-Python-2.7.18 pybind11/2.6.2 pybind11/2.6.0 pybind11/2.4.3-Python-3.8.2 pybind11/2.4.3-Python-3.7.4 |
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 PyCairo/1.20.1 PyCairo/1.18.2 |
Python bindings for the cairo library | |
| PYCHARM | PyCharm/2022.2.3 |
PyCharm Community Edition: Python IDE for Professional Developers | |
| PYCODESTYLE | pycodestyle/2.11.1 |
pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8. | |
| PYCUDA | PyCUDA/2021.1 |
PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python. | |
| PYCURL | PycURL/7.45.3 PycURL/7.45.2 PycURL/7.43.0.5-Python-3.7.4 |
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/2.7.4 pydantic/2.5.3 pydantic/1.10.4 pydantic/1.6.1-Python-3.9.6 |
Data validation and settings management using Python type hinting. | |
| PYDOT | pydot/1.4.2 |
Python interface to Graphviz's Dot language. | |
| 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/0.8.1.1 pyfaidx/0.7.1 pyfaidx/0.7.0 |
pyfaidx: efficient pythonic random access to fasta subsequences | |
| PYFFTW | pyFFTW/0.13.1 |
A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. | |
| PYFLAKES | Pyflakes/3.2.0 |
A simple program which checks Python source files for errors. | |
| PYGENOMETRACKS | pyGenomeTracks/3.8 |
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. | |
| 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/1.11 |
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. | |
| PYMATGEN | pymatgen/2022.0.4 |
Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. | |
| PYMC3 | PyMC3/3.11.1 |
Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano | |
| PYMOL | PyMOL/2.5.0 |
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! | |
| PYOMO | Pyomo/6.4.2 |
Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. | |
| PYOPENCL | PyOpenCL/2020.2.2-Python-3.9.6 |
PyOpenCL lets you access GPUs and other massively parallel compute devices from Python. | |
| PYOPENGL | PyOpenGL/3.1.7 PyOpenGL/3.1.6 PyOpenGL/3.1.5 |
PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. | |
| PYPROJ | pyproj/3.6.0 pyproj/3.3.1 pyproj/3.1.0 pyproj/2.6.1.post1-Python-3.8.2 |
Python interface to PROJ4 library for cartographic transformations | |
| PYPY | PyPy/3.8-v7.3.7 |
PyPy is a replacement for CPython. It implements Python 2.7.18, and 3.7.10. It supports all of the core language, passing the Python 2.7 test suite and almost all of the 3.7 test suite (with minor modifications) It supports most of the commonly used Python standard library modules. whatis([==[Homepage: https://www.pypy.org/ | |
| 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 PyQt5/5.15.4 PyQt5/5.15.1 PyQt5/5.15.1-Python-3.8.2 |
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. | |
| PYRO-API | pyro-api/0.1.2 |
Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. | |
| PYRO-PPL | pyro-ppl/1.5.2 |
Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. | |
| PYROSETTA | PyRosetta/4.release-387 PyRosetta/4.release-384 |
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/0.18.0 Pysam/0.17.0 Pysam/0.16.0.1 Pysam/0.16.0.1-Python-2.7.18 Pysam/0.15.3 |
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. | |
| PYSCAF | pyScaf/0.12a-Python-2.7.18 |
pyScaf orders contigs from genome assemblies utilising several types of information | |
| PYSEER | pyseer/1.3.11 |
Reimplemented in python of SEER: Sequence element enrichment analysis. | |
| PYSPOA | pyspoa/0.2.1 pyspoa/0.0.8 pyspoa/0.0.4-Python-3.7.4 |
Python bindings to spoa. | |
| PYSTAN | PyStan/2.19.1.1 |
Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo. | |
| PYTABLES | PyTables/3.9.2 PyTables/3.8.0 PyTables/3.6.1 PyTables/3.6.1-Python-3.7.4 |
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 | pytest/7.4.2 pytest/7.2.2 pytest/7.1.3 pytest/6.2.4 |
The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries. | |
| PYTEST-FLAKEFINDER | pytest-flakefinder/1.1.0 |
Runs tests multiple times to expose flakiness. | |
| PYTEST-RERUNFAILURES | 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-XDIST | pytest-xdist/3.3.1 pytest-xdist/2.5.0 pytest-xdist/2.3.0 |
xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters. | |
| PYTHIA | PYTHIA/8.309 PYTHIA/8.309-noROOT PYTHIA/8.307-Python-3.8.6 |
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/3.12.3 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/3.8.2 Python/3.7.4 Python/2.7.18 Python/2.7.18-bare Python/2.7.16 Python/2.7.16-bare Python/2.7.15 |
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/2024.06 Python-bundle-PyPI/2023.10 Python-bundle-PyPI/2023.06 |
Bundle of Python packages from PyPI | |
| PYTHON-IGRAPH | python-igraph/0.10.3 python-igraph/0.9.6 |
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 python-isal/0.11.1 python-isal/0.11.0 |
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/1.3.3 python-parasail/1.2.4 python-parasail/1.2-Python-3.7.4 |
Python Bindings for the Parasail C Library | |
| PYTORCH | PyTorch/2.7.0 PyTorch/2.7.0-CUDA-12.6.0 PyTorch/2.1.2 PyTorch/2.1.2-CUDA-12.1.1 PyTorch/1.12.1 PyTorch/1.12.1-CUDA-11.3.1 PyTorch/1.10.0 PyTorch/1.10.0-CUDA-11.3.1 PyTorch/1.9.0 PyTorch/1.9.0-imkl PyTorch/1.8.1 PyTorch/1.7.1 PyTorch/1.6.0-Python-3.7.4 |
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/2.5.2-PyTorch-2.1.2-CUDA-12.1.1 PyTorch-Geometric/2.5.0-PyTorch-2.1.2-CUDA-12.1.1 PyTorch-Geometric/2.0.1-PyTorch-1.9.0 |
PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. | |
| PYTORCH-LIGHTNING | PyTorch-Lightning/2.2.1-CUDA-12.1.1 PyTorch-Lightning/1.5.10-CUDA-11.3.1 PyTorch-Lightning/1.5.9 PyTorch-Lightning/1.5.9-CUDA-11.3.1 |
PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. | |
| PYTORCH3D | PyTorch3D/0.4.0-PyTorch-1.7.1 |
PyTorch3D is FAIR's library of reusable components for deep learning with 3D data. | |
| PYVCF | PyVCF/0.6.8-Python-2.7.16 |
A Variant Call Format reader for Python. | |
| PYWGCNA | PyWGCNA/2.0.2 |
PyWGCNA is a Python library designed to do weighted correlation network analysis (WGCNA). | |
| PYYAML | PyYAML/6.0.1 PyYAML/6.0 PyYAML/5.4.1 PyYAML/5.3.1 PyYAML/5.3 PyYAML/5.1.2 |
PyYAML is a YAML parser and emitter for the Python programming language. | |
| PYZMQ | PyZMQ/25.1.2 PyZMQ/25.1.1 PyZMQ/25.1.0 PyZMQ/24.0.1 PyZMQ/18.1.1-Python-3.7.4 |
Python bindings for ZeroMQ | |
| QCA | QCA/2.3.5 |
Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. | |
| QCAT | qcat/1.1.0-Python-3.7.4 |
qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files | |
| QCHEM | qchem/5.4.2-openmp qchem/5.4.0-openmp qchem/5.3.2-openmp |
Q-Chem 5.4.2 release environment module | |
| QGIS | QGIS/3.28.1 |
QGIS is a user friendly Open Source Geographic Information System (GIS) | |
| 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 | QIIME2/2024.10-Metagenome QIIME2/2024.10-Pathogenome QIIME2/2024.10-Amplicon QIIME2/2022.8 |
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. | |
| QRUPDATE | qrupdate/1.1.2 |
qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. | |
| QSCINTILLA | QScintilla/2.11.6 |
QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control | |
| QT5 | Qt5/5.15.13 Qt5/5.15.10 Qt5/5.15.7 Qt5/5.15.5 Qt5/5.15.2 Qt5/5.14.2 Qt5/5.14.1 Qt5/5.13.1 |
Qt is a comprehensive cross-platform C++ application framework. | |
| QT5WEBKIT | Qt5Webkit/5.212.0-alpha4 |
Qt Port of WebKit. WebKit is an open source web browser engine. | |
| QT6 | Qt6/6.6.3 Qt6/6.5.2 |
Qt is a comprehensive cross-platform C++ application framework. | |
| QTCONSOLE | Qtconsole/5.5.1 |
A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more. | |
| QTKEYCHAIN | QtKeychain/0.14.2 QtKeychain/0.13.2 |
QtKeychain is a Qt API to store passwords and other secret data securely. | |
| QTPY | QtPy/2.4.1 |
QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide. | |
| QUALIMAP | Qualimap/2.2.1-R-4.1.2 |
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. | |
| QUANTUMESPRESSO | QuantumESPRESSO/7.2 QuantumESPRESSO/6.8 |
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/5.0.2-Python-2.7.18quast/5.2.0 |
QUAST stands for QUality ASsessment Tool. It evaluates genome/metagenome assemblies by computing various metrics. The current QUAST toolkit includes the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, QUAST-LG, the extension for large genomes (e.g., mammalians), and Icarus, the interactive visualizer for these tools. | |
| 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 Qwt/6.1.5 |
The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. | |
| R | R/4.4.1 R/4.3.3 R/4.3.2 R/4.3.1 R/4.2.1 R/4.2.0 R/4.1.2 R/4.1.0 R/4.0.5 R/4.0.3 R/4.0.0 R/3.6.3 |
R is a free software environment for statistical computing and graphics. | HPRC Docs |
| R-BUNDLE-BIOCONDUCTOR | R-bundle-Bioconductor/3.14-R-4.1.2 |
Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. | |
| R-BUNDLE-CRAN | R-bundle-CRAN/2024.06 R-bundle-CRAN/2024.06-with-Cairo R-bundle-CRAN/2023.12 |
Bundle of R packages from CRAN | |
| R-RMPI | R-Rmpi/0.7-2 |
An interface (wrapper) to MPI. It also provides interactive R manager and worker environment. | |
| RACON | Racon/1.5.0 Racon/1.4.13 |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. | |
| RAGEL | ragel/6.10 |
Ragel compiles executable finite state machines from regular languages. | |
| RAGTAG | RagTag/2.1.0 RagTag/2.0.1 |
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/1.1.0-20240409 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 | |
| RASPA2 | RASPA2/2.0.47 |
RASPA is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials. | |
| RASTERIO | rasterio/1.2.10 rasterio/1.1.7-Python-3.8.2 |
Rasterio reads and writes geospatial raster data. | |
| RAXML | RAxML/8.2.13-avx2 RAxML/8.2.12-pthreads-sse3 RAxML/8.2.12-pthreads-avx2 |
RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. | |
| RAXML-NG | RAxML-NG/1.2.0 RAxML-NG/1.1.0 RAxML-NG/1.0.2 |
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/2.6.2 Ray-project/2.2.0 |
Ray is a fast and simple framework for building and running distributed applications. | |
| RCLONE | rclone/1.66.0 rclone/1.63.1-amd64 |
Rclone is a command line program to sync files and directories to and from a variety of online storage services | HPRC Docs |
| RDFLIB | RDFlib/7.0.0 RDFlib/6.2.0 RDFlib/5.0.0 |
RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information. | |
| RDKIT | RDKit/2024.03.3 |
RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. | |
| RE2 | RE2/2024-03-01 RE2/2023-08-01 RE2/2023-03-01 RE2/2022-06-01 RE2/2022-02-01re2/2023-11-01 |
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/3.1 re2c/3.0 re2c/2.2 re2c/2.1.1 re2c/2.0.3 re2c/1.3 re2c/1.2.1 |
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/7.0.8 Redis/6.2.6 |
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/4.5.1 redis-py/4.3.3 |
The Python interface to the Redis key-value store. | |
| RELION | RELION/5.0.0-CUDA-12.1.1 RELION/5.0.0-CUDA-11.8.0 RELION/4.0.0 RELION/4.0.0-CUDA-11.8.0 RELION/4.0.0-CUDA-11.7.0 |
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). | |
| REPEATMASKER | RepeatMasker/4.1.7-p1 RepeatMasker/4.1.4 RepeatMasker/4.1.2-p1 |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | |
| REPEATMODELER | RepeatModeler/2.0.6 RepeatModeler/2.0.5 |
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 ) | |
| REVBAYES | RevBayes/1.2.1 |
RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. | |
| RFDIFFUSION-SCHEDULES | RFdiffusion-schedules/1.1.0 |
RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper https://www.biorxiv.org/content/10.1101/2022.12.09.519842v1 Schedule files are available in $RFDIFFUSION_SCHEDULES | |
| RFDIFFUSIONAA | RFDiffusionAA/2024.03.13 |
A unified structure prediction and design approach for assemblies containing proteins, nucleic acids, small molecules, metals, and chemical modifications. | |
| RIBODETECTOR | RiboDetector/0.3.1-CUDA-11.3.1 |
RiboDetector - Accurate and rapid RiboRNA sequences Detector based on deep learning | |
| RIOXARRAY | rioxarray/0.11.1 rioxarray/0.1.1-Python-3.8.2 |
geospatial xarray extension powered by rasterio | |
| RJAGS | rjags/4-12-R-4.1.2 |
The rjags package is an interface to the JAGS library. | |
| RLWRAP | rlwrap/0.45.2 |
rlwrap is a 'readline wrapper', a small utility that uses the GNU readline library to allow the editing of keyboard input for any command. I couldn't find anything like it when I needed it, so I wrote this one back in 1999. By now, there are (and, in hindsight, even then there were) a number of good readline wrappers around, like rlfe, distributed as part of the GNU readline library, and the amazing socat (http://freecode.com/projects/socat). You should consider rlwrap especially when you need user-defined completion (by way of completion word lists) and persistent history, or if you want to program 'special effects' using the filter mechanism. rlwrap compiles and runs on a fairly wide range of Unix-like systems. | |
| RMBLAST | RMBlast/2.14.1 RMBlast/2.13.0 RMBlast/2.11.0 |
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. | |
| RNALYSIS | RNAlysis/3.8.0 RNAlysis/3.3.0 |
RNAlysis is a Python-based software for analyzing RNA sequencing data. | |
| RNAQUAST | rnaQUAST/2.2.2 |
rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software. | |
| RNASTRUCTURE | RNAstructure/6.2 |
RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. | |
| ROARY | Roary/3.13.0 |
Rapid large-scale prokaryote pan genome analysis | |
| ROCKSDB | RocksDB/8.11.3 RocksDB/7.9.2 RocksDB/6.29.5 |
A Persistent Key-Value Store for Flash and RAM Storage | |
| ROCM-CMAKE | rocm-cmake/4.5.0 |
ROCM cmake modules provides cmake modules for common build tasks needed for the ROCM software stack | |
| ROCM-COMPILERSUPPORT | ROCm-CompilerSupport/4.5.0 |
The compiler support repository provides various Lightning Compiler related services | |
| ROCM-SMI | rocm-smi/4.5.0 |
The ROCm System Management Interface Library, or ROCm SMI library, is part of the Radeon Open Compute ROCm software stack. It is a C library for Linux that provides a user space interface for applications to monitor and control GPU applications. | |
| ROCR-RUNTIME | ROCR-Runtime/4.5.0 |
The user-mode API interfaces and libraries necessary for host applications to launch compute kernels to available HSA ROCm kernel agents | |
| ROCT-THUNK-INTERFACE | ROCT-Thunk-Interface/4.5.0 |
The user-mode API interfaces used to interact with the ROCk driver | |
| ROOT | ROOT/6.26.10 ROOT/6.26.06 ROOT/6.14.06 |
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/3.9-Python-2.7.18 |
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/2.11 |
rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use | |
| RPY2 | rpy2/3.5.7 |
rpy2 is an interface to R running embedded in a Python process. | |
| RSEM | RSEM/1.3.3 |
RNA-Seq by Expectation-Maximization | |
| RSEQC | RSeQC/4.0.0 |
RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. | |
| RUBY | Ruby/3.3.0 Ruby/3.2.2 Ruby/3.0.5 Ruby/3.0.1 Ruby/2.7.1 |
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/1.81.0 Rust/1.78.0 Rust/1.76.0 Rust/1.75.0 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/1.42.0 |
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. | |
| S-LANG | S-Lang/2.3.0 |
S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software. It provides facilities required by interactive applications such as display/screen management, keyboard input, keymaps, and so on. | |
| SALMON | Salmon/1.10.3 Salmon/1.10.1 Salmon/1.9.0 Salmon/1.7.0 Salmon/1.4.0 Salmon/0.8.2 |
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. | |
| SAMCLIP | samclip/0.4.0 |
Filter SAM file for soft and hard clipped alignments. | |
| SAMTOOLS | SAMtools/1.21 SAMtools/1.20 SAMtools/1.19.2 SAMtools/1.18 SAMtools/1.17 SAMtools/1.16.1 SAMtools/1.14 SAMtools/1.13 SAMtools/1.12 SAMtools/1.11 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/1.0.1 |
ScaFaCoS is a library of scalable fast coulomb solvers. | |
| SCALAPACK | ScaLAPACK/2.2.0-fb ScaLAPACK/2.1.0 ScaLAPACK/2.1.0-fb ScaLAPACK/2.1.0-bf ScaLAPACK/2.0.2 ScaLAPACK/2.0.2-OpenBLAS-0.3.1 |
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/1.9.1 |
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. | |
| SCIKIT-BIO | scikit-bio/0.5.7 |
scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. | |
| SCIKIT-BUILD | scikit-build/0.17.6 scikit-build/0.17.2 scikit-build/0.16.7 scikit-build/0.15.0 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/0.9.3 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-FDA | scikit-fda/0.7.1 |
This package offers classes, methods and functions to give support to Functional Data Analysis in Python. Includes a wide range of utils to work with functional data, and its representation, exploratory analysis, or preprocessing, among other tasks such as inference, classification, regression or clustering of functional data. | |
| SCIKIT-IMAGE | scikit-image/0.22.0 scikit-image/0.21.0 scikit-image/0.19.3 scikit-image/0.19.1 scikit-image/0.18.3 scikit-image/0.18.1 scikit-image/0.16.2-Python-3.7.4 |
scikit-image is a collection of algorithms for image processing. | |
| SCIKIT-LEARN | scikit-learn/1.4.0 scikit-learn/1.3.1 scikit-learn/1.2.1 scikit-learn/1.1.2 scikit-learn/1.0.1 scikit-learn/0.24.2 scikit-learn/0.23.2 scikit-learn/0.23.1-Python-3.8.2 scikit-learn/0.22.1 scikit-learn/0.21.3-Python-3.7.4 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 |
| SCIKIT-MISC | scikit-misc/0.1.4 |
Miscellaneous tools for data analysis and scientific computing | |
| SCIPY | scipy/1.4.1-Python-3.7.4 |
SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python. | |
| SCIPY-BUNDLE | SciPy-bundle/2024.05 SciPy-bundle/2023.11 SciPy-bundle/2023.07 SciPy-bundle/2023.02 SciPy-bundle/2022.05 SciPy-bundle/2021.10 SciPy-bundle/2021.10-Python-2.7.18 SciPy-bundle/2021.05 SciPy-bundle/2020.11 SciPy-bundle/2020.11-Python-2.7.18 SciPy-bundle/2020.03-Python-3.8.2 SciPy-bundle/2020.03-Python-2.7.18 SciPy-bundle/2019.10-Python-3.7.4 SciPy-bundle/2019.10-Python-2.7.16 |
Bundle of Python packages for scientific software | |
| SCIPY_TAMU | SciPy_tamu/2021.10-Python-3.8.6 |
Bundle of Python packages for scientific software | |
| SCNIC | SCNIC/0.6.3 |
SCNIC is a package for the generation and analysis of cooccurrence (positive correlation) networks with compositional data. | |
| 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/4.2.0 SCons/4.0.1 SCons/3.1.2 SCons/3.1.1 |
SCons is a software construction tool. | |
| SCOTCH | SCOTCH/7.0.4 SCOTCH/7.0.3 SCOTCH/7.0.1 SCOTCH/6.1.2 SCOTCH/6.1.0 SCOTCH/6.0.9 |
Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. | |
| SCREED | screed/1.1.3 |
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | |
| 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 | SDL2/2.28.5 SDL2/2.28.2 SDL2/2.26.3 SDL2/2.26.2 SDL2/2.0.22 SDL2/2.0.20 SDL2/2.0.14 SDL2/2.0.10 |
SDL: Simple DirectMedia Layer, a cross-platform multimedia library | |
| SDSL | SDSL/2.1.1-20191211 |
The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. | |
| SE3-TRANSFORMER | SE3-Transformer/1.1.0-CUDA-12.1.1 |
The SE(3)-Transformer is a Graph Neural Network using a variant of self-attention for 3D points and graphs processing. | |
| SEABORN | Seaborn/0.13.2 Seaborn/0.12.2 Seaborn/0.12.1 Seaborn/0.11.2 Seaborn/0.11.1 Seaborn/0.10.0-Python-3.7.4 Seaborn/0.9.1-Python-2.7.18 |
Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. | |
| SEAVIEW | SeaView/5.0.5 |
SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. | |
| SEGMENTATION-MODELS | segmentation-models/1.0.1-Python-3.7.4 |
Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow. | |
| SENTENCEPIECE | SentencePiece/0.2.0 SentencePiece/0.1.97 |
Unsupervised text tokenizer for Neural Network-based text generation. | |
| SEPP | SEPP/4.5.5 SEPP/4.5.1 SEPP/4.4.0 |
SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. | |
| SEQAN | SeqAn/2.4.0 |
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. | |
| SEQKIT | SeqKit/2.3.1 |
SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation | |
| SEQLIB | SeqLib/1.2.0 |
C++ interface to HTSlib, BWA-MEM and Fermi. | |
| SEQMAP | SeqMap/1.0.12 |
SeqMap is a tool for mapping large amount of oligonucleotide to the genome. | |
| SEQTK | seqtk/1.4 seqtk/1.3 |
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. | |
| SEQWISH | seqwish/0.7.9 |
seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments. | |
| 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 | |
| SETUPTOOLS-RUST | setuptools-rust/1.9.0 setuptools-rust/1.8.0 setuptools-rust/1.6.0 setuptools-rust/1.5.2 setuptools-rust/1.3.0 setuptools-rust/0.12.1 |
setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython. | |
| SHAP | SHAP/0.42.1 |
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. | |
| SHAPEIT4 | SHAPEIT4/4.1.3 |
SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. | |
| SHAPELY | Shapely/2.0.1 Shapely/1.8.2 Shapely/1.8a1 Shapely/1.7.1-Python-3.8.2 |
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. | |
| SIBELIA | Sibelia/3.0.7 |
Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. | |
| SIGNALP | SignalP/6.0g.fast SignalP/6.0g-fast-CUDA-12.1.1 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. | |
| SIONLIB | SIONlib/1.7.7-tools |
SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. | |
| SIP | SIP/6.8.1 |
SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. | |
| SISCONE | siscone/3.0.5 |
Hadron Seedless Infrared-Safe Cone jet algorithm | |
| SLEPC | SLEPc/3.15.1 SLEPc/3.12.2-Python-3.7.4 |
SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. | |
| SLICER | Slicer/5.6.2 |
3D Slicer is a free, open source software for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes; and planning and navigating image-guided procedures. | |
| SMITHWATERMAN | smithwaterman/20160702 |
smith-waterman-gotoh alignment algorithm. | |
| SMRT-LINK | SMRT-Link/13.1.0.221970-cli-tools-only SMRT-Link/11.0.0.146107-cli-tools-only SMRT-Link/10.1.0.119588-cli-tools-only SMRT-Link/7.0.1.66975-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 | |
| SNAKEMAKE | snakemake/8.4.2 snakemake/7.32.3 snakemake/7.22.0 snakemake/6.10.0 snakemake/6.1.0 |
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. | |
| SNAP | SNAP/1.0.0-Linux64 |
SNAP is a fast and accurate aligner for short DNA reads. | |
| 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. | |
| SNAPPY | snappy/1.2.1 snappy/1.1.10 snappy/1.1.9 snappy/1.1.8 snappy/1.1.7 |
Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. | |
| SNIPPY | snippy/4.6.0-R-4.1.2 |
Rapid haploid variant calling and core genome alignment | |
| SNP-SITES | snp-sites/2.5.1 |
Finds SNP sites from a multi-FASTA alignment file. | |
| SNPEFF | snpEff/5.0e-Java-11 |
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). | |
| 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. | |
| SPACK | Spack/0.21.2 Spack/0.17.2 |
Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. | |
| SPACY | spaCy/3.1.7-Python-3.7.4 spaCy/2.2.3-Python-3.7.4 |
Industrial-strength Natural Language Processing (NLP) in Python. | |
| SPADES | SPAdes/4.0.0 SPAdes/3.15.5 SPAdes/3.15.4 SPAdes/3.15.3 SPAdes/3.15.2-Python-2.7.18 SPAdes/3.14.1-Python-3.8.2 |
Genome assembler for single-cell and isolates data sets | |
| SPALN | spaln/2.4.03 |
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/3.2.1 |
Spark is Hadoop MapReduce done in memory | |
| SPARSEHASH | sparsehash/2.0.4 sparsehash/2.0.3 |
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. | |
| SPECTRA | SpectrA/1.0.1 |
Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. | |
| SPEEDSEQ | SpeedSeq/0.1.2-Python-2.7.16 |
A flexible framework for rapid genome analysis and interpretation. | |
| SPGLIB | spglib/2.0.2 |
Spglib is a C library for finding and handling crystal symmetries. | |
| SPGLIB-PYTHON | spglib-python/2.1.0 spglib-python/2.0.0 spglib-python/1.16.0 |
Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. | |
| SPINE | Spine/0.3.2 |
Spine is a program for identification of the conserved core genome of bacteria and other small genome organisms. | |
| SPOA | spoa/4.1.0 spoa/4.0.7 spoa/4.0.0 |
Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences | |
| SPYTHON | spython/0.3.13 spython/0.3.0 spython/0.1.15 |
Singularity Python (spython) is the Python API for working with Singularity containers. | |
| SQLALCHEMY | SQLAlchemy/2.0.29 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/3.45.3 SQLite/3.43.1 SQLite/3.42.0 SQLite/3.39.4 SQLite/3.38.3 SQLite/3.36 SQLite/3.35.4 SQLite/3.33.0 SQLite/3.31.1 SQLite/3.29.0 SQLite/3.24.0 |
SQLite: SQL Database Engine in a C Library | |
| SRA-TOOLKIT | SRA-Toolkit/3.1.1 SRA-Toolkit/3.0.10 SRA-Toolkit/3.0.3 SRA-Toolkit/3.0.2-centos_linux64 SRA-Toolkit/3.0.0-centos_linux64 |
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/3.1.2 |
Single Read Paired Read Indel Substitution Minimizer | |
| SSPACE_BASIC | SSPACE_Basic/2.1.1-Python-2.7.18 |
SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension | |
| SST-CORE | sst-core/14.0.0 |
The Structural Simulation Toolkit (SST) was developed to explore innovations in highly concurrent systems where the ISA, microarchitecture, and memory interact with the programming model and communications system. | |
| 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/2.68 Stacks/2.66 Stacks/2.64 Stacks/2.62 |
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. | |
| STADEN | Staden/2.0.0b11-2016 |
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | |
| STAR | STAR/2.7.11b STAR/2.7.11a STAR/2.7.10b STAR/2.7.9a STAR/2.7.7a STAR/2.7.6a STAR/2.7.2b |
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. | |
| STAR-CCM+ | 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 |
| STATSMODELS | statsmodels/0.14.1 statsmodels/0.14.0 statsmodels/0.13.1 statsmodels/0.12.1 |
Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. | |
| STD_COMPAT | std_compat/0.0.7 |
LibStdCompat is a set of compatibility headers for C++ 14, 17, and 20 for C++11. | |
| STITCH | STITCH/1.6.7 |
STITCH - Sequencing To Imputation Through Constructing Haplotypes | |
| STRACE | strace/5.14 |
strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state. | |
| STRINGTIE | 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 Structure/2.3.4-Java-8.452-GUI |
The program structure is a free software package for using multi-locus genotype data to investigate population structure. | |
| STRUMPACK | STRUMPACK/6.1.0 |
STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner for both dense and sparse systems using low-rank structured factorization with randomized sampling. | |
| SUBPHASER | SubPhaser/1.2.6 |
SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers | |
| SUBREAD | Subread/2.0.8 Subread/2.0.7 Subread/2.0.3 Subread/2.0.2 Subread/2.0.0 |
High performance read alignment, quantification and mutation discovery | |
| SUBVERSION | Subversion/1.14.2 Subversion/1.14.1 Subversion/1.14.0 Subversion/1.10.7 |
Subversion is an open source version control system. | |
| SUITESPARSE | SuiteSparse/7.7.0-METIS-5.1.0 SuiteSparse/5.13.0-METIS-5.1.0 SuiteSparse/5.10.1-METIS-5.1.0 SuiteSparse/5.10.1-METIS-5.1.0-CUDA-11.3.1 SuiteSparse/5.8.1-METIS-5.1.0 SuiteSparse/5.7.1-METIS-5.1.0 SuiteSparse/5.6.0-METIS-5.1.0 |
SuiteSparse is a collection of libraries to manipulate sparse matrices. | |
| SUNDIALS | SUNDIALS/6.3.0 SUNDIALS/5.7.0 |
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers | |
| SUPERLU_DIST | 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. | |
| SVTYPER | svtyper/0.5.2-Python-2.7.16 |
Bayesian genotyper for structural variants | |
| SWIG | SWIG/4.1.1 SWIG/4.0.2 SWIG/4.0.1 |
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 SyRI/1.6.3 |
Synteny and Rearrangement Identifier (SyRI). | |
| SZ | SZ/2.1.12.5 |
Error-bounded lossy compressor for HPC data. | |
| SZ3 | SZ3/3.1.7 |
A modular error-bounded lossy compression framework for scientific datasets. | |
| SZIP | Szip/2.1.1 |
Szip compression software, providing lossless compression of scientific data | |
| TABIXPP | tabixpp/1.1.2 tabixpp/1.1.0 |
C++ wrapper to tabix indexer | |
| TAICHI | Taichi/1.2.1 |
Taichi Lang is an open-source, imperative, parallel programming language for high-performance numerical computation. It is embedded in Python and uses just-in-time (JIT) compiler frameworks, for example LLVM, to offload the compute-intensive Python code to the native GPU or CPU instructions. | |
| TANTAN | tantan/40 |
tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences | |
| TASSEL | TASSEL/5.2.82-Java-1.8 |
TASSEL provides tools to investigate relationships between phenotypes and genotypes | |
| TAXATOR-TK | taxator-tk/1.3.3 |
A set of programs for the taxonomic analysis of nucleotide sequence data | |
| TBB | tbb/2021.13.0 tbb/2021.11.0 tbb/2021.10.0 tbb/2021.5.0 tbb/2021.4.0 tbb/2020.3 tbb/2020.2 tbb/2020.1 tbb/2019_U9 |
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-linux64 tbl2asn/20220613-linux64 tbl2asn/20220427-linux64 |
Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank | |
| TCL | Tcl/8.6.14 Tcl/8.6.13 Tcl/8.6.12 Tcl/8.6.11 Tcl/8.6.10 Tcl/8.6.9 Tcl/8.6.8 |
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/1.2.5 |
TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary. | |
| TCSH | tcsh/6.24.07 tcsh/6.24.01 tcsh/6.24.00 tcsh/6.22.04 tcsh/6.22.03 tcsh/6.22.02 |
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. | |
| TDB | tdb/1.4.10 |
This is a simple database API. It was inspired by the realisation that in Samba we have several ad-hoc bits of code that essentially implement small databases for sharing structures between parts of Samba. | |
| TENSORBOARD | tensorboard/2.15.1 tensorboard/2.10.0 tensorboard/2.8.0 |
TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs. | |
| TENSORBOARDX | tensorboardX/2.6.2.2 tensorboardX/2.5.1 tensorboardX/2.2-PyTorch-1.7.1 |
Tensorboard for PyTorch. | |
| TENSORFLOW | TensorFlow/2.15.1-CUDA-12.1.1 TensorFlow/2.13.0 TensorFlow/2.11.0-CUDA-11.7.0 TensorFlow/2.8.4 TensorFlow/2.7.1 TensorFlow/2.7.1-CUDA-11.4.1 TensorFlow/2.6.0 TensorFlow/2.6.0-CUDA-11.3.1 TensorFlow/2.5.3-CUDA-11.3.1 TensorFlow/2.5.0 TensorFlow/2.4.1 TensorFlow/2.3.1-Python-3.8.2 TensorFlow/2.2.0-Python-3.7.4 TensorFlow/2.1.0-Python-3.7.4 TensorFlow/1.15.2-Python-3.7.4 |
An open-source software library for Machine Intelligence | HPRC Docs |
| TENSORFLOW-PROBABILITY | tensorflow-probability/0.19.0-CUDA-11.7.0 tensorflow-probability/0.12.1 |
TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis. | |
| TENSORRT | TensorRT/8.6.0.12-CUDA-12 TensorRT/8.6.0.12-CUDA-11 |
An SDK for high-performance deep learning inference, includes a deep learning inference optimizer and runtime that delivers low latency and high throughput for inference applications. | |
| TENSORSTORE | tensorstore/0.1.65 |
TensorStore is an open-source C++ and Python software library designed for storage and manipulation of large multi-dimensional arrays. | |
| TERMCAP | termcap/1.3.1 |
Termcap is a library and data base that enables programs to use display terminals in a terminal-independent manner. | |
| TESMALL | TEsmall/2.0.6 TEsmall/2.0.3 |
A pipeline for profiling TE-derived small RNAs. | |
| TETGEN | TetGen/1.6.0 |
A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator | |
| 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. | |
| THEANO | Theano/1.1.2-PyMC Theano/1.0.4-Python-3.7.4 |
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. | |
| THERMO-CALC | Thermo-Calc/2024.2 Thermo-Calc/2024.1 Thermo-Calc/2023.2 Thermo-Calc/2023.1 |
Thermocalc is a software package for thermodynamic calculations. It is widely used for a variety of calculations. | |
| TIDK | tidk/0.2.41 |
tidk is a toolkit to identify and visualise telomeric repeats for the Darwin Tree of Life genomes. | |
| 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/8.6.14 Tk/8.6.13 Tk/8.6.12 Tk/8.6.11 Tk/8.6.10 Tk/8.6.9 |
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/3.11.5 Tkinter/3.11.3 Tkinter/3.10.8 Tkinter/3.10.4 Tkinter/3.9.6 Tkinter/3.9.5 Tkinter/3.8.6 Tkinter/3.8.2 Tkinter/3.7.4 Tkinter/2.7.18 Tkinter/2.7.16 |
Tkinter module, built with the Python buildsystem | |
| TMHMM | TMHMM/2.0c TMHMM/2.0c-Perl-5.30.2 |
Prediction of transmembrane helices in proteins. | |
| TOGA | TOGA/2024.05.26 |
TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost. | |
| TOGL | Togl/2.0 |
A Tcl/Tk widget for OpenGL rendering. | |
| TOKENIZERS | tokenizers/0.15.2 tokenizers/0.3.0 |
Fast State-of-the-Art Tokenizers optimized for Research and Production | |
| TOMLI | tomli/2.0.1 |
Tomli is a Python library for parsing TOML. | |
| TORCHINFO | torchinfo/1.5.2-PyTorch-1.7.1 |
" Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network. | |
| TORCHVISION | torchvision/0.16.0 torchvision/0.16.0-CUDA-12.1.1 torchvision/0.13.1-PyTorch-1.12.1 torchvision/0.11.3-CUDA-11.3.1 torchvision/0.11.1-CUDA-11.3.1 torchvision/0.9.1-PyTorch-1.9.0-fosscuda-2020b-imkl torchvision/0.9.1-PyTorch-1.8.1 torchvision/0.8.2-PyTorch-1.7.1 |
Datasets, Transforms and Models specific to Computer Vision | |
| TORNADO | tornado/6.4 tornado/6.3.2 |
Tornado is a Python web framework and asynchronous networking library. | |
| TOXCODAN-GENOME | ToxCodAn-Genome/2024.11.14 |
ToxCodAn-Genome is a computational tool designed to annotate toxin genes in genomes of venomous lineages. | |
| TPMCALCULATOR | TPMCalculator/0.0.4 |
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. | |
| TQDM | tqdm/4.66.2 tqdm/4.66.1 tqdm/4.64.1 tqdm/4.64.0 tqdm/4.62.3 tqdm/4.61.2 tqdm/4.56.2 tqdm/4.47.0 tqdm/4.41.1 |
A fast, extensible progress bar for Python and CLI | |
| TRANSDECODER | TransDecoder/5.7.1 TransDecoder/5.5.0 |
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. | |
| TREEMIX | TreeMix/1.13 |
TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. | |
| TRF | TRF/4.09.1 TRF/4.09-linux64 |
Tandem Repeats Finder: a program to analyze DNA sequences. | |
| TRIMAL | trimAl/1.4.1 |
EVB, FEP and LIE simulator. | |
| TRIMMOMATIC | Trimmomatic/0.39-Java-11 Trimmomatic/0.38-Java-1.8 |
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/0.6.7 Trim_Galore/0.6.6-Python-3.8.2 Trim_Galore/0.6.6-Python-2.7.18 Trim_Galore/0.6.5-Java-11-Python-3.7.4 |
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/2.15.1 |
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. | |
| TRINOTATE | Trinotate/4.0.1 |
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome. | |
| TRNASCAN-SE | tRNAscan-SE/2.0.12 |
tRNAscan-SE is the most widely employed tool for identifying and annotating tRNA genes in genomes. | |
| 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 TWL-NINJA/0.97-cluster_only |
Nearly Infinite Neighbor Joining Application. | |
| TXG | txg/2.0.0 |
The 10x Genomics Cloud CLI is a command line interface (CLI) that allows you to upload input files to projects in your 10x Genomics account, create projects from the command line, and manage other tasks related to your 10x Genomics account. | |
| 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. | |
| UCSCTEST | ucsctest/1.0 |
Tools from the UCSC browser.. | |
| UCSCTOOLS | UCSCtools/2021.08.21 UCSCtools/2020.12.01 UCSCtools/2020.12.01-test |
Tools from the UCSC browser.. | |
| UCX | UCX/1.16.0 UCX/1.15.0 UCX/1.15.0-rc4 UCX/1.14.1 UCX/1.13.1 UCX/1.12.1 UCX/1.11.2 UCX/1.11.0 UCX/1.10.0 UCX/1.9.0 UCX/1.9.0-CUDA-11.1.1 UCX/1.8.0 UCX/1.8.0-CUDA-11.0.2 |
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-rc4-CUDA-12.4.1 UCX-CUDA/1.14.1-CUDA-12.1.1 UCX-CUDA/1.14.1-CUDA-11.8.0 UCX-CUDA/1.13.1-CUDA-12.0.0 UCX-CUDA/1.13.1-CUDA-11.8.0 UCX-CUDA/1.12.1-CUDA-11.7.0 UCX-CUDA/1.11.2-CUDA-11.4.1 UCX-CUDA/1.11.0-CUDA-11.4.1 UCX-CUDA/1.10.0-CUDA-11.3.1 |
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/2.2.26 |
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/0.5.5 umap-learn/0.5.3 |
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. | |
| UMI-TOOLS | UMI-tools/1.0.1-Python-3.8.2 |
Tools for handling Unique Molecular Identifiers in NGS data sets | |
| 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. | |
| 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. | |
| UNISON | unison/2.53.0 |
Unison is a file-synchronization tool. It allows two replicas of a collection of files and directories to be stored on different hosts (or different disks on the same host), modified separately, and then brought up to date by propagating the changes in each replica to the other. | |
| 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. | |
| UPCXX | upcxx/2022.9.0 upcxx/2020.3.0 upcxx/2020.3.0-CUDA-11.7.0 |
UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming, and is designed to interoperate smoothly and efficiently with MPI, OpenMP, C++/POSIX threads, CUDA, ROCm/HIP and other HPC frameworks. It leverages GASNet-EX to deliver low-overhead, fine-grained communication, including Remote Memory Access (RMA) and Remote Procedure Call (RPC). | |
| UPROOT | Uproot/4.1.9-Python-3.8.6 Uproot/4.1.2-Python-3.8.6 |
Uproot is a reader and a writer of the ROOT file format using only Python and Numpy. | |
| 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/2.6.1 utf8proc/2.5.0 |
utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. | |
| UTHASH | uthash/2.3.0 |
A hash table for C structures. | |
| UTIL-LINUX | 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 util-linux/2.35 util-linux/2.34 |
Set of Linux utilities | |
| VALGRIND | Valgrind/3.21.0 Valgrind/3.16.1 |
Valgrind: Debugging and profiling tools | |
| VASP | vasp/6.3.2 vasp/6.3.2-VTST-195-VASPsol vasp/6.3.2-VTST-195-VASPsol-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 For additional details, use the module help command - Homepage: http://www.vasp.at | HPRC Docs |
| VAWK | vawk/0.0.1-Python-2.7.16 |
An awk-like VCF parser. vawk command syntax is exactly the same as awk syntax with a few additional features. | |
| VCFLIB | vcflib/1.0.9-R-4.3.2 vcflib/1.0.3-R-4.1.2 |
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. | |
| VEP | VEP/107 |
Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP. | |
| VESTA | VESTA/3.5.8-gtk3 |
VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies. | |
| VG | VG/1.65.0 VG/1.56.0 VG/1.48.0 VG/1.36.0 |
variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods | |
| VIBRANT | VIBRANT/1.2.1-Python-3.7.4 |
Virus Identification By iteRative ANnoTation | |
| VIRALRECALL | ViralRecall/2024.07.05 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 VirSorter2/2.2.4-dev |
VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. | |
| VIRTUALENV | virtualenv/20.26.2 virtualenv/20.24.6 virtualenv/20.23.1 virtualenv/20.4.6 |
A tool for creating isolated virtual python environments. | |
| VIRTUALGL | VirtualGL/3.1 VirtualGL/3.0 |
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 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. | |
| VISPY | VisPy/0.12.2 |
VisPy is a high-performance interactive 2D/3D data visualization library leveraging the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets. | |
| VMD | VMD/1.9.4a57 VMD/1.9.4a51 VMD/1.9.3-Python-2.7.18 |
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. | |
| VSCODE | VSCode/1.88.1 |
Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos. | |
| VSEARCH | VSEARCH/2.22.1 |
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. | |
| 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 VTK/9.1.0 VTK/9.0.1 VTK/8.2.0-Python-3.8.2 VTK/8.2.0-Python-3.7.4 |
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. | |
| VTUNE | VTune/2022.2.0 |
Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. | |
| VULKANSDK | VulkanSDK/1.3.280.1 VulkanSDK/1.3.261.1 VulkanSDK/1.3.250.1 VulkanSDK/1.3.236.0 VulkanSDK/1.2.189.0 |
The Khronos Vulkan API is an explicit, low-overhead, cross-platform graphics and compute API. | |
| WANDB | wandb/0.16.1 wandb/0.13.4 |
CLI and Python API for Weights and Biases (wandb), a tool for visualizing and tracking your machine learning experiments. | |
| WANNIER90 | Wannier90/3.1.0 |
A tool for obtaining maximally-localised Wannier functions | |
| WAYLAND | Wayland/1.23.0 Wayland/1.22.0 Wayland/1.21.0 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+/2.37.1 |
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. | |
| WEBPROXY | WebProxy/0000 |
WebProxy module sets up web and ftp proxy 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. | |
| WFMASH | wfmash/0.10.7 |
A DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. | |
| WGET | wget/1.21.3 wget/1.21.2 wget/1.21.1 wget/1.20.3 |
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. | |
| WGSIM | wgsim/20111017 |
Wgsim is a small tool for simulating sequence reads from a reference genome. | |
| WHATSHAP | WhatsHap/2.2 WhatsHap/1.4 |
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. | |
| WIGGLETOOLS | WiggleTools/1.2.11 |
The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc). | |
| WINNOWMAP | Winnowmap/2.03 |
Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques. | |
| WOLFPSORT | WoLFPSort/0.2 |
Protein Subcellular Localization Prediction | |
| WPEBACKEND-FDO | wpebackend-fdo/1.15.90 wpebackend-fdo/1.13.1 |
WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. | |
| WPS | WPS/4.3.1-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 |
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/4.3.3-dmpar WRF/4.3-smpar WRF/4.3-dmpar WRF/3.9.1.1-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 |
| WTDBG2 | wtdbg2/2.5 |
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. | |
| WXPYTHON | wxPython/4.2.1 wxPython/4.2.0 |
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/3.2.1 wxWidgets/3.2.0 wxWidgets/3.1.4 wxWidgets/3.1.3 wxWidgets/3.0.3 |
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 | X11/20240607 X11/20231019 X11/20230603 X11/20221110 X11/20220504 X11/20210802 X11/20210518 X11/20201008 X11/20200222 X11/20190717 |
The X Window System (X11) is a windowing system for bitmap displays | |
| X264 | x264/20231019 x264/20230226 x264/20220620 x264/20210613 x264/20210414 x264/20201026 x264/20191217 x264/20190925 |
x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. | |
| X265 | x265/3.5 x265/3.3 x265/3.2 |
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/0.20.1 xarray/0.19.0 xarray/0.16.1-Python-3.8.2 |
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. | |
| XCB-PROTO | xcb-proto/1.11 |
The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. | |
| XCRYSDEN | XCrySDen/1.6.2 |
XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. | |
| XENGSORT | xengsort/2.0.4 |
This tool, xengsort, uses 3-way bucketed Cuckoo hashing to efficiently solve the xenograft sorting problem. | |
| 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. | |
| XEXTPROTO | xextproto/7.3.0 |
XExtProto protocol headers. | |
| XFCE4 | xfce4/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XFCE4-APPFINDER | xfce4-appfinder/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XFCE4-DEV-TOOLS | xfce4-dev-tools/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XFCE4-PANEL | xfce4-panel/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XFCE4-SETTINGS | xfce4-settings/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XFCONF | xfconf/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XFDESKTOP | xfdesktop/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XFWM4 | xfwm4/4.18.0 |
Xfce is a lightweight desktop environment for UNIX-like operating systems. It aims to be fast and low on system resources, while still being visually appealing and user friendly. | |
| XLSXWRITER | XlsxWriter/3.0.8 XlsxWriter/1.4.3 |
A Python module for creating Excel XLSX files | |
| XML-COMPILE | XML-Compile/1.63 |
Perl module for compilation based XML processing | |
| XML-LIBXML | XML-LibXML/2.0210 XML-LibXML/2.0209 XML-LibXML/2.0208 XML-LibXML/2.0207 XML-LibXML/2.0206 XML-LibXML/2.0205 XML-LibXML/2.0201 |
Perl binding for libxml2 | |
| XMLTODICT | xmltodict/0.13.0 |
Python module that makes working with XML feel like you are working with JSON. | |
| XORG-MACROS | xorg-macros/1.20.1 xorg-macros/1.20.0 xorg-macros/1.19.3 xorg-macros/1.19.2 |
X.org macros utilities. | |
| XPMEM | xpmem/61c39ef |
XPMEM is a Linux kernel module that enables a process to map the memory of another process into its virtual address space. | |
| XPROP | xprop/1.2.7 xprop/1.2.6 xprop/1.2.5 xprop/1.2.4 |
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 | |
| XTALOPT | XtalOpt/r12.3 |
XtalOpt is a free and truly open source evolutionary algorithm designed for a priori crystal structure prediction. | |
| XTB | xtb/6.7.1 xtb/6.5.1 xtb/6.2.3 |
xtb - An extended tight-binding semi-empirical program package. | |
| XTENSOR | xtensor/0.25.0 |
xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions. | |
| XTRANS | xtrans/1.3.5 |
xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. | |
| XVFB | Xvfb/21.1.9 Xvfb/21.1.8 Xvfb/21.1.6 Xvfb/21.1.3 Xvfb/1.20.13 Xvfb/1.20.11 Xvfb/1.20.9 |
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/9.1.0307 xxd/9.0.2112 xxd/9.0.1696 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/5.4.5 XZ/5.4.4 XZ/5.4.2 XZ/5.2.7 XZ/5.2.5 XZ/5.2.5-NextPolish XZ/5.2.4 |
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. | |
| YAFF | yaff/1.6.0-Python-3.8.2 yaff/1.6.0-Python-3.7.4 |
Yaff stands for 'Yet another force field'. It is a pythonic force-field code. | |
| 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. | |
| YAK | yak/0.1 |
Yak is initially developed for two specific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads. | |
| YASM | Yasm/1.3.0 |
Yasm: Complete rewrite of the NASM assembler with BSD license | |
| YAXT | YAXT/0.9.2 YAXT/0.9.1 YAXT/0.6.2 |
Yet Another eXchange Tool | |
| Z3 | Z3/4.13.0 Z3/4.12.2 Z3/4.12.2-Python-3.11.3 Z3/4.10.2 Z3/4.10.2-Python-3.10.4 Z3/4.8.16 Z3/4.8.12 Z3/4.8.11 Z3/4.8.10 |
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. | |
| ZARR | zarr/2.13.3 zarr/2.11.0 zarr/2.8.1 |
Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. | |
| 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/4.3.3 ZeroMQ/4.3.2 |
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. | |
| ZFP | zfp/0.5.5 |
zfp is a compressed format for representing multidimensional floating-point and integer arrays. zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and write large data sets to and from disk. | |
| ZIP | Zip/3.0 |
Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality | |
| ZLIB | zlib/1.3.1 zlib/1.2.13 zlib/1.2.12 zlib/1.2.11 zlib/1.2.8 |
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 zstd/1.4.5 zstd/1.4.4 |
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. |