Software Modules on the Terra Cluster

Last Updated: Mon May 10 13:32:55 CDT

The available software for the Terra cluster is listed in the table. Click on any software package name to get more information such as the available versions, additional documentation if available, etc.

Name Description
4ti2'A software package for algebraic, geometric and combinatorial problems on linear spaces'
AAF'AAF constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. URL: https://sourceforge.net/projects/aaf-phylogeny/'
ABAQUS'Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.'
ABINIT'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. URL: https://www.abinit.org/'
ABRicate'Mass screening of contigs for antimicrobial and virulence genes URL: https://github.com/tseemann/abricate'
absl-py'Abseil Python Common Libraries'
ABySS'Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler URL: https://www.bcgsc.ca/platform/bioinfo/software/abyss'
ACTC'ACTC converts independent triangles into triangle strips or fans.'
AdapterRemoval'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.'
ADDA'ADDA is an open-source parallel implementation of the discrete dipole approximation, capable to simulate light scattering by particles of arbitrary shape and composition in a wide range of particle sizes. URL: https://github.com/adda-team/adda/wiki'
adjustText'A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps. URL: https://github.com/Phlya/adjustText'
ADOL-C'The package ADOL-C (Automatic Differentiation by OverLoading in C--) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C--. The resulting derivative evaluation routines may be called from C/C--, Fortran, or any other language that can be linked with C. URL: https://projects.coin-or.org/ADOL-C'
AFNI'AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. URL: http://afni.nimh.nih.gov/'
AGEnt' 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. URL: https://github.com/egonozer/AGEnt'
AGFusion'AGFusion is a python package for annotating gene fusions from the human or mouse genomes. URL: https://github.com/murphycj/AGFusion'
aiohttp'" Async http client/server framework '
Albacore' Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms.'
ALFA'ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism. URL: https://github.com/biocompibens/ALFA'
Algorithm-Loops' Algorithm::Loops - Looping constructs: NestedLoops, MapCar-, Filter, and NextPermute- URL: https://metacpan.org/pod/Algorithm::Loops'
almosthere'Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program. URL: https://github.com/horta/almosthere'
Amara'Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML. URL: https://pypi.org/project/Amara'
amask'amask is a set of tools to to determine the affinity of MPI processes and OpenMP threads in a parallel environment.'
AmberMini'A stripped-down set of just antechamber, sqm, and tleap. URL: https://github.com/choderalab/ambermini'
AMOS'The AMOS consortium is committed to the development of open-source whole genome assembly software'
AMPL' The AMPL system supports the entire optimization modeling lifecycle — formulation, testing, deployment, and maintenance — in an integrated way that promotes rapid development and reliable results. URL: https://ampl.com/'
AMPL-MP' An open-source library for mathematical programming. URL: https://github.com/ampl/mp'
AMPL-Py' AMPL API is an interface that allows developers to access the features of the AMPL interpreter from within a programming language URL: https://github.com/ampl/amplpy Compatible modules: Python/2.7.16-GCCcore-8.3.0 (default)'
AMR++'MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data URL: https://github.com/meglab-metagenomics/amrplusplus_v2'
AMRFinderPlus'NCBI Antimicrobial Resistance Gene Finder Plus URL: https://github.com/ncbi/amr/wiki'
Anaconda'Anaconda Distribution gives superpowers to people that change the world with high performance, cross-platform Python and R that includes the best innovative data science from open source.'
Anaconda2'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. URL: https://www.anaconda.com'
Anaconda3'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. URL: https://www.anaconda.com'
Anaconda-Jupyter'Anaconda Distribution gives superpowers to people that change the world with high performance, cross-platform Python and R that includes the best innovative data science from open source.'
Ancestry_HMM'a hidden Markhov model'
angsd'Program for analysing NGS data.'
Annif'Annif is a multi-algorithm automated subject indexing tool for libraries, archives and museums. URL: https://github.com/NatLibFi/Annif'
ANSYS' 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. URL: http://www.ansys.com'
AnsysEM'ANSYS Electromagnetics Suite'
ant'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. URL: https://ant.apache.org/'
antiSMASH'antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. URL: https://github.com/antismash/antismash'
ANTLR'ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C--, or Python actions.'
ANTs'ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. URL: https://stnava.github.io/ANTs/'
anvio'An analysis and visualization platform for 'omics data. URL: https://merenlab.org/software/anvio/'
any2fasta'Convert various sequence formats to FASTA URL: https://github.com/tseemann/any2fasta'
apex'A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch URL: https://github.com/nvidia/apex'
APR'Apache Portable Runtime (APR) libraries. URL: https://apr.apache.org/'
APR-util'Apache Portable Runtime (APR) util libraries. URL: https://apr.apache.org/'
ARAGORN'a program to detect tRNA genes and tmRNA genes in nucleotide sequences URL: http://mbio-serv2.mbioekol.lu.se/ARAGORN/'
archspec'A library for detecting, labeling, and reasoning about microarchitectures URL: https://github.com/archspec/archspec'
ARGoS'A parallel, multi-engine simulator for heterogeneous swarm robotics URL: http://www.argos-sim.info'
argparse' Python command-line parsing library'
argtable' Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. '
ARIBA'ARIBA is a tool that identifies antibiotic resistant genes by running local assemblies URL: https://github.com/sanger-pathogens/ariba'
Arlequin'Arlequin: An Integrated Software for Population Genetics Data Analysis URL: http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html'
Armadillo'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. URL: https://arma.sourceforge.net/'
ARPACK++'Arpackpp is a C-- interface to the ARPACK Fortran package, which implements the implicit restarted Arnoldi method for iteratively solving large-scale sparse eigenvalue problems.'
arpack-ng'ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. URL: https://github.com/opencollab/arpack-ng'
ArrayFire' ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.'
Arriba'Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. URL: https://github.com/suhrig/arriba'
Arrow'Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform for in-memory data. URL: https://arrow.apache.org'
ArrowGrid_HPRC'The distribution is a parallel wrapper around the Arrow consensus framework within the SMRT Analysis Software. The pipeline is composed of bash scripts, an example input fofn which shows how to input your bax.h5 files (you give paths without the .1.bax.h5), and how to launch the pipeline. The input can be either BAX.h5 or BAM files (only P6-C4 chemistry or newer) and requires SMRTportal 3.1-. It can also run the older Quiver algorithm if requested in the CONFIG file on the P6-C4 chemistry data.'
ART' ART is a set of simulation tools to generate synthetic next-generation sequencing reads'
ARTS' ARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly for the different sensors. URL: http://www.radiativetransfer.org/'
ArviZ'Exploratory analysis of Bayesian models with Python URL: https://github.com/arviz-devs/arviz'
ASAP3'ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). URL: https://wiki.fysik.dtu.dk/asap/'
ASCENDS'ASCENDS: Advanced data SCiENce toolkit for Non-Data Scientists URL: https://github.com/ornlpmcp/ASCENDS'
ASE'ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. URL: https://wiki.fysik.dtu.dk/ase'
assimp' 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. URL: https://github.com/assimp/assimp'
Assimulo'Assimulo is a simulation package for solving ordinary differential equations.'
ASTRID'ASTRID-2 is a method for estimating species trees from gene trees. URL: https://github.com/pranjalv123/ASTRID'
astropy'The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. URL: https://www.astropy.org/'
asyncoro' Python framework for concurrent, distributed, asynchronous network programming with coroutines, asynchronous completions and message passing.'
ATK' 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. URL: https://developer.gnome.org/atk/'
Atkmm' Atkmm is the official C-- interface for the ATK accessibility toolkit library. '
ATOMEYE(description not available)
AtomPAW'AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library. URL: http://users.wfu.edu/natalie/papers/pwpaw/man.html'
atools'Tools to make using job arrays a lot more convenient. URL: https://github.com/gjbex/atools'
at-spi2-atk'AT-SPI 2 toolkit bridge URL: https://wiki.gnome.org/Accessibility'
at-spi2-core' Assistive Technology Service Provider Interface. URL: https://wiki.gnome.org/Accessibility'
attr'Commands for Manipulating Filesystem Extended Attributes URL: https://savannah.nongnu.org/projects/attr'
augur'Pipeline components for real-time phylodynamic analysis URL: https://github.com/nextstrain/augur'
AUGUSTUS'AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences URL: http://bioinf.uni-greifswald.de/augustus/'
Autoconf' 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. URL: https://www.gnu.org/software/autoconf/'
AutoDock' 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. URL: https://autodock.scripps.edu/'
AutoDock_Vina' AutoDock Vina is an open-source program for doing molecular docking. URL: http://vina.scripps.edu/index.html'
AutoGrid' 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. URL: https://autodock.scripps.edu/'
Automake'Automake: GNU Standards-compliant Makefile generator URL: https://www.gnu.org/software/automake/automake.html'
AutoMap'Tool to find regions of homozygosity (ROHs) from sequencing data. URL: https://github.com/mquinodo/AutoMap'
Autotools' This bundle collect the standard GNU build tools: Autoconf, Automake and libtool URL: https://autotools.io'
Bader'A fast algorithm for doing Bader's analysis on a charge density grid.'
bagpipes'Bayesian Analysis of Galaxies for Physical Inference and Parameter EStimation is a state of the art Python code for modelling galaxy spectra and fitting spectroscopic and photometric observations. URL: https://bagpipes.readthedocs.io/en/latest'
BAMM'BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a program for modeling complex dynamics of speciation, extinction, and trait evolution on phylogenetic trees. URL: http://bamm-project.org'
bam-readcount'Count DNA sequence reads in BAM files'
BamTools'BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.'
BamUtil'BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.'
barrnap'Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes.'
basemap'The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python'
BatMeth2'An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping. URL: https://github.com/GuoliangLi-HZAU/BatMeth2'
BayeScan'BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.'
Bazel'Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. URL: https://bazel.io/'
bbFTP'bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. bbFTP main features are: - Encoded username and password at connection - SSH and Certificate authentication modules - Multi-stream transfer - Big windows as defined in RFC1323 - On-the-fly data compression - Automatic retry - Customizable time-outs - Transfer simulation - AFS authentication integration - RFIO interface URL: https://software.in2p3.fr/bbftp/'
BBMap'BBMap short read aligner, and other bioinformatic tools. URL: https://sourceforge.net/projects/bbmap/'
BCALM'de Bruijn graph compaction in low memory'
BCEL' The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give users a convenient way to analyze, create, and manipulate (binary) Java class files (those ending with .class). URL: https://commons.apache.org/proper/commons-bcel/'
BCFtools'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 URL: https://www.htslib.org/'
bcgTree'Automatized phylogenetic tree building from bacterial core genomes.'
bcl2fastq2'bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. URL: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
bcolz'bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes. URL: https://bcolz.blosc.org/en/latest/'
BDBag'The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles.'
beagle-lib'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 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. URL: http://beast2.org/'
BeautifulSoup'Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. URL: https://www.crummy.com/software/BeautifulSoup'
BEDOPS'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: 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. URL: https://bedtools.readthedocs.io/'
behave'behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a software project.'
BerkeleyGW'The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. URL: https://www.berkeleygw.org'
BFC'BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.'
BiG-SCAPE'BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. URL: https://bigscape-corason.secondarymetabolites.org/index.html'
BinSanity'BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes. URL: https://github.com/edgraham/BinSanity/wiki'
binutils'binutils: GNU binary utilities URL: https://directory.fsf.org/project/binutils/'
bioawk' 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. '
biobambam2'Tools for processing BAM files'
Bio-DB-HTS'Read files using HTSlib including BAM/CRAM, Tabix and BCF database files URL: https://metacpan.org/release/Bio-DB-HTS'
Bio-Easel' 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. URL: https://github.com/EddyRivasLab/easel'
Bio-EUtilities'BioPerl low-level API for retrieving and storing data from NCBI eUtils URL: https://github.com/bioperl/bio-eutilities'
Biogeme' Biogeme is an open source freeware designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models. '
bioinfokit'The bioinfokit toolkit aimed to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments. URL: https://github.com/reneshbedre/bioinfokit'
biom-format' The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. URL: http://biom-format.org'
Bio-MLST-Check'Multilocus sequence typing by blast using the schemes from PubMLST. URL: https://github.com/sanger-pathogens/mlst_check'
BioPerl'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. URL: https://bioperl.org/'
BioPP' Bio-- is a set of C-- libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio-- is Object Oriented and is designed to be both easy to use and computer efficient. Bio-- intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. URL: https://github.com/BioPP/bpp-core'
Biopython'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. URL: https://www.biopython.org'
BioRuby'BioRuby is an open source Ruby library for developing bioinformatics software. URL: https://github.com/bioruby/bioruby'
BioServices'Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols). URL: http://bioservices.readthedocs.io/'
Bismark'A tool to map bisulfite converted sequence reads and determine cytosine methylation states'
Bison' 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. URL: https://www.gnu.org/software/bison'
bitarray'bitarray provides an object type which efficiently represents an array of booleans'
BLASR'The PacBio® long read aligner URL: https://github.com/PacificBiosciences/blasr'
BLAST'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+'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. URL: https://blast.ncbi.nlm.nih.gov/'
BLAT'BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. URL: https://genome.ucsc.edu/FAQ/FAQblat.html'
Blender'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. URL: https://www.blender.org/'
BLIS'AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. URL: https://developer.amd.com/amd-cpu-libraries/blas-library/'
Blitz++' Blitz-- is a (LGPLv3-) licensed meta-template library for array manipulation in C-- with a speed comparable to Fortran implementations, while preserving an object-oriented interface'
BlobTools' A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. '
Blosc'Blosc, an extremely fast, multi-threaded, meta-compressor library URL: https://www.blosc.org/'
bml' The basic matrix library (bml) is a collection of various matrix data formats (in dense and sparse) and their associated algorithms for basic matrix operations.'
bmtagger'Best Match Tagger for removing human reads from metagenomics datasets URL: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/'
bnpy'Bayesian nonparametric machine learning for python provides code for training popular clustering models on large datasets. The focus is on Bayesian nonparametric models based on the Dirichlet process, but it also provides parametric counterparts. URL: https://github.com/bnpy/bnpy'
bokeh'Statistical and novel interactive HTML plots for Python URL: https://github.com/bokeh/bokeh'
BoltzTraP2'band-structure interpolator and transport coefficient calculator'
Bonito'Convolution Basecaller for Oxford Nanopore Reads URL: https://github.com/nanoporetech/bonito'
Bonmin'Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization. URL: https://coin-or.github.io/Ipopt'
Boost'Boost provides free peer-reviewed portable C-- source libraries. URL: https://www.boost.org/'
Boost.Python'Boost.Python is a C-- library which enables seamless interoperability between C-- and the Python programming language. URL: https://boostorg.github.io/python Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.17-GCCcore-9.3.0'
Botan' Botan (Japanese for peony) is a cryptography library written in C--11 and released under the permissive Simplified BSD license.'
Bottleneck'Fast NumPy array functions written in C URL: https://kwgoodman.github.io/bottleneck-doc'
Bowtie'Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. URL: http://bowtie-bio.sourceforge.net/index.shtml'
Bowtie2' 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. URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
BreakDancer'BreakDancer is a Perl/C-- package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads URL: http://gmt.genome.wustl.edu/packages/breakdancer'
breseq'breseq is a computational pipeline for the analysis of short-read re-sequencing data URL: https://barricklab.org/breseq'
bsddb3'bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects. URL: https://pypi.org/project/bsddb3/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
BSMAPz'Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study. URL: https://github.com/zyndagj/BSMAPz'
Bsoft' Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. URL: http://lsbr.niams.nih.gov/bsoft/'
buildenv' 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 <this module name> URL: None'
BUSCO'Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50. URL: https://busco.ezlab.org/'
BUStools'bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. URL: https://github.com/BUStools/bustools'
BWA'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-meth'Fast and accurante alignment of BS-Seq reads. URL: https://github.com/brentp/bwa-meth Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
bwidget'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. URL: https://core.tcl-lang.org/bwidget/home'
BWISE'de Bruijn Workflow using Integral information of Short pair End reads'
bx-python'The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses. URL: https://github.com/bxlab/bx-python'
byacc' Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.'
bzip2' 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. URL: https://sourceware.org/bzip2'
cachetools' This module provides various memoizing collections and decorators, including variants of the Python Standard Library’s @lru_cache function decorator. URL: https://pypi.python.org/pypi/cachetools/'
cactus'Cactus is a reference-free whole-genome multiple alignment program.'
CAFE' The purpose of CAFE (Computational Analysis of gene Family Evolution) is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. URL: https://github.com/hahnlab/CAFE'
CAFExp' The purpose of CAFE (Computational Analysis of gene Family Evolution) is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. URL: https://github.com/hahnlab/CAFE'
Caffe' Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. URL: https://github.com/BVLC/caffe'
cairo'Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB URL: https://cairographics.org'
cairocffi'cffi-based cairo bindings for Python'
cairomm' The Cairomm package provides a C-- interface to Cairo. '
calc' Calc is an arbitrary precision C-like arithmetic system that is a calculator, an algorithm-prototyper, and a mathematical research tool. URL: http://isthe.com/chongo/tech/comp/calc'
Calendrical'Calendrical module is for calendrical calculations. URL: https://www.funaba.org/code#calendrical'
Calib'Calib clusters paired-end reads using their barcodes and sequences. Calib is suitable for amplicon sequencing where a molecule is tagged, then PCR amplified with high depth, also known as Unique Molecule Identifier (UMI) sequencing. URL: https://github.com/vpc-ccg/calib'
Cantera'Chemical kinetics, thermodynamics, and transport tool suite'
canu'Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing URL: https://canu.readthedocs.io'
CapnProto'Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.'
Cargo'The Rust package manager'
carputils'carputils is a Python framework for generating and running openCARP examples. URL: https://git.opencarp.org/openCARP/carputils'
Cartopy'Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy. URL: https://scitools.org.uk/cartopy/docs/latest/'
CastXML'CastXML is a C-family abstract syntax tree XML output tool.'
cath-resolve-hits' 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. URL: https://github.com/UCLOrengoGroup/cath-tools'
causallift' CausalLift: Python package for Uplift Modeling in real-world business; applicable for both A/B testing and observational data URL: https://github.com/Minyus/causallift'
causalml' Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML URL: https://github.com/uber/causalml'
CaVEMan'SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib'
Cbc'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. URL: https://github.com/coin-or/Cbc'
CBLAS'C interface to the BLAS URL: https://www.netlib.org/blas/'
ccache'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 URL: https://ccache.dev/'
cclib' cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner. URL: https://cclib.github.io/'
cctools'The Cooperative Computing Tools (cctools) is a software package for enabling large scale distributed computing on clusters, clouds, and grids.'
CD-HIT'CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. URL: https://github.com/weizhongli/cdhit'
cDNA_Cupcake'cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.'
CDO'CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. URL: https://code.zmaw.de/projects/cdo'
cdsapi'Climate Data Store API URL: https://pypi.org/project/cdsapi Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
Centrifuge'Classifier for metagenomic sequences URL: https://ccb.jhu.edu/software/centrifuge'
CESM(description not available)
CESM-deps'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. URL: http://www.cesm.ucar.edu/models/cesm2/'
cffi'Python http for humans'
CFITSIO'CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. URL: https://heasarc.gsfc.nasa.gov/fitsio/'
cftime'Time-handling functionality from netcdf4-python URL: https://github.com/Unidata/cftime'
CGAL'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. URL: https://www.cgal.org/'
cget'Cmake package retrieval. This can be used to download and install cmake packages'
Cgl'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. URL: https://github.com/coin-or/Cgl'
CGmapTools'Command-line Toolset for Bisulfite Sequencing Data Analysis URL: https://cgmaptools.github.io/'
CGNS'The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. URL: https://cgns.github.io/'
CharLS'CharLS is a C-- implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios.'
Check' Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format. URL: https://libcheck.github.io/check/'
CheckM'CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. URL: https://github.com/Ecogenomics/CheckM'
Cheetah'Cheetah is an open source template engine and code generation tool.'
CheMPS2'CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.'
chewBBACA'chewBBACA stands for "BSR-Based Allele Calling Algorithm". chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. URL: https://github.com/B-UMMI/chewBBACA'
Chimera' 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. URL: https://www.cgl.ucsf.edu/chimera/'
ChimPipe'ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution. URL: https://chimpipe.readthedocs.org/'
Chromaprint'Chromaprint is the core component of the AcoustID project. It's a client-side library that implements a custom algorithm for extracting fingerprints from any audio source. URL: https://acoustid.org/chromaprint'
ciftify'The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets'
CIRCexplorer2'CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. URL: http://circexplorer2.readthedocs.io/'
Circos'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. URL: http://www.circos.ca/'
cisTEM' cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.'
CITE-seq-Count'A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment. URL: https://github.com/Hoohm/CITE-seq-Count'
Clang'C, C--, Objective-C compiler, based on LLVM. Does not include C-- standard library -- use libstdc-- from GCC. URL: https://clang.llvm.org/'
Clang-Python-bindings'Python bindings for libclang URL: https://clang.llvm.org'
CLAPACK'C version of LAPACK'
CLHEP' 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. URL: https://proj-clhep.web.cern.ch/proj-clhep/'
click'A simple wrapper around optparse for powerful command line utilities.'
CLISP' Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. URL: https://clisp.sourceforge.io/'
Clp'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. URL: https://github.com/coin-or/Clp'
Clustal-Omega' 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 is a general purpose multiple sequence alignment program for DNA or proteins. URL: https://www.ebi.ac.uk/Tools/msa/clustalw2/'
CMake' CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. URL: https://www.cmake.org'
CmdlineGL' CmdlineGL is an interpreter for a "text-friendly" variation of a subset of the OpenGL 1.4 API, Glut API, and FTGL "C" API.'
CNVkit'A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. URL: http://github.com/etal/cnvkit'
CNVnator' a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads URL: https://github.com/abyzovlab/CNVnator'
CoinUtils'CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. URL: https://github.com/coin-or/CoinUtils'
colorama'Cross-platform colored terminal text.'
colorspace'Color Space Manipulation'
Comsol'COMSOL Multiphysics is a general-purpose simulation software for modeling designs, devices, and processes in all fields of engineering, manufacturing, and scientific research. '
CONCOCT'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. URL: https://concoct.readthedocs.io'
configurable-http-proxy'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. URL: https://github.com/jupyterhub/configurable-http-proxy'
CONN' CONN is a Matlab-based cross-platform software for the computation, display, and analysis of functional connectivity in fMRI (fcMRI). URL: http://www.conn-toolbox.org/'
ConvergeCFD'Converge CFD software by Convergent Science '
CoordgenLibs'Schrodinger-developed 2D Coordinate Generation URL: https://github.com/schrodinger/coordgenlibs'
Coot'Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. URL: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot'
Core'EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. URL: https://easybuilders.github.io/easybuild'
Coreutils'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. URL: https://www.gnu.org/software/coreutils/'
corner'Make some beautiful corner plots. URL: https://corner.readthedocs.io/en/latest/'
coverage' Coverage.py is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not.'
covid-sim' This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London. URL: https://github.com/mrc-ide/covid-sim'
CP2K'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. URL: https://www.cp2k.org/'
CPLEX'IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability. URL: https://www.ibm.com/analytics/cplex-optimizer Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
CppUnit' CppUnit is the C-- port of the famous JUnit framework for unit testing. URL: https://freedesktop.org/wiki/Software/cppunit/'
cram'Cram is a functional testing framework for command line applications. URL: https://bitheap.org/cram Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
crb-blast'Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation. URL: https://github.com/cboursnell/crb-blast'
CRF++'CRF-- is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF-- is designed for generic purpose and will be applied to a variety of NLP tasks, such as Named Entity Recognition, Information Extraction and Text Chunking. '
CRISPResso2' CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. URL: https://github.com/pinellolab/CRISPResso2'
CrossMap'CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF. URL: http://crossmap.sourceforge.net'
CRPropa'CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment. URL: https://crpropa.desy.de'
CSBDeep'CSBDeep is a toolbox for Content-aware Image Restoration (CARE). URL: https://csbdeep.bioimagecomputing.com/'
csvkit'csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. URL: https://github.com/wireservice/csvkit'
ctags'Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.'
ctffind'Program for finding CTFs of electron micrographs. URL: https://grigoriefflab.umassmed.edu/ctffind4'
CubeGUI' Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer. URL: https://www.scalasca.org/software/cube-4.x/download.html'
CubeLib' Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C-- library component and command-line tools. URL: https://www.scalasca.org/software/cube-4.x/download.html'
CubeWriter' Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component. URL: https://www.scalasca.org/software/cube-4.x/download.html'
CUDA'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. URL: https://developer.nvidia.com/cuda-toolkit'
CUDAcore'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. URL: https://developer.nvidia.com/cuda-toolkit'
cuDNN'The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. URL: https://developer.nvidia.com/cudnn'
Cufflinks'Transcript assembly, differential expression, and differential regulation for RNA-Seq URL: http://cole-trapnell-lab.github.io/cufflinks/'
CUnit'Automated testing framework for C.'
curc-bench' curc-bench is a regression testing benchmark suite developed at and for University of Colorado Boulder Research Computing. It uses linpack, stream, and osu-micro-benchmarks.'
curc-bench-terra'TAMU HPRC settings for using curc-bench on terra'
cURL' 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. URL: https://curl.haxx.se'
cutadapt'Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. URL: https://opensource.scilifelab.se/projects/cutadapt/'
CVXOPT'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. URL: https://cvxopt.org'
CVXPY' 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. URL: https://www.cvxpy.org/'
CWPSU' Seismic Unix is an open source seismic utilities package supported by the Center for Wave Phenomena (CWP) at the Colorado School of Mines (CSM). '
Cycler'Composable style cycles'
Cython'The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. URL: https://pypi.python.org/pypi/Cython/'
cytosim'Cytosim is a cytoskeleton simulation engine written in C-- working on Mac OS, GNU/Linux and Windows (with Cygwin). URL: https://github.com/nedelec/cytosim'
cyvcf2'cython - htslib == fast VCF and BCF processing URL: https://github.com/brentp/cyvcf2 Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
Dakota' Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models.'
DALIGNER'The Dresden AZZembLER for long read DNA projects URL: https://github.com/thegenemyers/DALIGNER'
dask'Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. URL: https://dask.org/'
DAS_Tool'DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. URL: https://github.com/cmks/DAS_Tool'
datamash'GNU datamash performs basic numeric, textual and statistical operations on input data files URL: https://www.gnu.org/software/datamash/'
davix'The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols. URL: https://dmc.web.cern.ch/projects/davix/home'
DAZZ_DB'The Dazzler Database library URL: https://github.com/thegenemyers/DALIGNER'
DB'Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. URL: https://www.oracle.com/technetwork/products/berkeleydb'
DBD-mysql'Perl binding for MySQL URL: https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm'
DB_File'Perl5 access to Berkeley DB version 1.x. URL: https://perldoc.perl.org/DB_File.html'
DBG2OLC'DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies'
DBus' 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. URL: https://dbus.freedesktop.org/'
dbus-glib'D-Bus is a message bus system, a simple way for applications to talk to one another.'
dcm2niix'dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.'
DCMTK'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.'
deal.II'deal.II is a C-- program library targeted at the computational solution of partial differential equations using adaptive finite elements. URL: https://www.dealii.org'
deconf'decomposition (deconfounding) of OMICS datasets in heterogeneous tissues URL: http://web.cbio.uct.ac.za/~renaud/CRAN/'
DeconICA'Deconvolution of transcriptome through Immune Component Analysis (DeconICA) is an R package for identifying immune-related signals in transcriptome through deconvolution or unsupervised source separation methods. URL: https://urszulaczerwinska.github.io/DeconICA'
deepdiff'DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. URL: https://deepdiff.readthedocs.io/en/latest/'
DeepSurv' DeepSurv is a deep learning approach to survival analysis. URL: https://github.com/jaredleekatzman/DeepSurv'
deepTools'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. URL: https://deeptools.readthedocs.io/'
Delft3D' Delft3D is Open Source Software. To enhance collaboration, to combine the unique expertise of researchers worldwide and to further expand the modelling suite, the source code of Delft3D 4 Suite can be downloaded. The following modules are available: FLOW - MOR - WAVE - WAQ (DELWAQ) - PART. URL: http://oss.deltares.nl/web/delft3d'
DeMixT'Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms. URL: https://bioinformatics.mdanderson.org/main/DeMixT'
DendroPy'A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. URL: https://pypi.python.org/pypi/DendroPy/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
DETONATE'DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.'
devel'Development/test modules for TAMU HPRC'
DFTB+'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. URL: https://www.dftb-plus.info'
DFT-D3'DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. URL: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english'
dftd3-lib'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. URL: https://github.com/dftbplus/dftd3-lib'
DHSVM-PNNL' DHSVM—the Distributed Hydrology Soil Vegetation Model—was developed in the early 1990s (Wigmosta et al., 1994(Offsite link)) by the Pacific Northwest National Laboratory (PNNL) and the University of Washington (UW) to numerically represent with high spatial resolution the effects of local weather, topography, soil type, and vegetation on hydrologic processes within watersheds. URL: https://dhsvm.pnnl.gov/'
DIAMOND'DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. URL: https://github.com/bbuchfink/diamond'
dichromat'Color Schemes for Dichromats'
digest'Create Compact Hash Digests of R Objects'
dill'dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. URL: https://pypi.org/project/dill/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
DIRAC'DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations URL: http://www.diracprogram.org'
dispy' Distributed and Parallel Computing with/for Python.'
distributed'Dask.distributed is a lightweight library for distributed computing in Python. It extends both the concurrent.futures and dask APIs to moderate sized clusters.'
DIYABC'a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers URL: http://www1.montpellier.inra.fr/CBGP/diyabc'
DL_POLY_Classic'DL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package. URL: https://gitlab.com/DL_POLY_Classic/dl_poly'
DMTCP'DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. URL: http://dmtcp.sourceforge.net/index.html'
dm-tree'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. URL: https://github.com/deepmind/tree Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
DOLFIN'DOLFIN is the C--/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.'
Doris'Delft object-oriented radar interferometric software'
dotNET-SDK'.NET is a free, cross-platform, open source developer platform for building many different types of applications. URL: https://www.microsoft.com/net/'
double-conversion'Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. URL: https://github.com/google/double-conversion'
DoubletFinder'R package for detecting doublets in single-cell RNA sequencing data URL: https://github.com/chris-mcginnis-ucsf/DoubletFinder'
Doxygen' 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. URL: https://www.doxygen.org'
dropEST'Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements. URL: https://github.com/stan-dev/rstan'
DSA'Digital Sorting Algorithm URL: https://github.com/zhandong/DSA'
Dsuite'Fast calculation of the ABBA-BABA statistics across many populations/species URL: https://github.com/millanek/Dsuite'
dtcmp' Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI. URL: https://github.com/llnl/dtcmp'
dtcwt'Dual-Tree Complex Wavelet Transform library for Python URL: https://github.com/rjw57/dtcwt'
dxpy'DNAnexus Platform API bindings for Python'
E2P2'Ensemble-based Enzyme Prediction Program (E2P2) predicts metabolic enzymes in a sequenced genome. URL: https://pmn.dpb.carnegiescience.edu/'
earthengine-api'Python and JavaScript bindings for calling the Earth Engine API'
EasyBuild'EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. URL: https://easybuilders.github.io/easybuild'
EasyBuild-terra'EasyBuild environment variables for building system software on terra.tamu.edu'
EasyBuild-terra-devel'EasyBuild environment variables for building test system software on terra.tamu.edu'
EasyBuild-terra-myeb'User EasyBuild environment for terra.tamu.edu in $SCRATCH/eb'
EasyBuild-terra-restricted-hprc'EasyBuild environment variables for building restricted software for HPRC on terra.tamu.edu'
EasyBuild-terra-SCRATCH'User EasyBuild environment for terra.tamu.edu in $SCRATCH/eb'
ecCodes'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). URL: https://software.ecmwf.int/wiki/display/ECC/ecCodes-Home'
EDirect'The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). URL: https://www.ncbi.nlm.nih.gov/books/NBK25501'
edlib'Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. URL: https://martinsos.github.io/edlib'
eggnog-mapper'eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments'
Eigen'Eigen is a C-- template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. URL: https://eigen.tuxfamily.org'
EIGENSOFT'The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. URL: http://www.hsph.harvard.edu/alkes-price/software/'
elastix' elastix: a toolbox for rigid and nonrigid registration of images. '
elfutils' The elfutils project provides libraries and tools for ELF files and DWARF data. URL: https://elfutils.org/'
Elk'An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. URL: http://elk.sourceforge.net/'
ELPA'Eigenvalue SoLvers for Petaflop-Applications . URL: https://elpa.rzg.mpg.de'
ELPH' ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). URL: http://ccb.jhu.edu/software/ELPH/index.shtml'
ELSI'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. URL: https://wordpress.elsi-interchange.org/'
Emacs'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. URL: https://www.gnu.org/software/emacs/'
EMAN2' EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. URL: https://blake.bcm.edu/emanwiki/EMAN2'
EMBOSS'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 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! URL: https://dfm.io/emcee'
EMU'EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets URL: http://www.popgen.dk/software/index.php/EMU'
enaBrowserTool'enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required. URL: https://github.com/enasequence/enaBrowserTools/'
entos'entos is a software package that enables ab initio molecular dynamics calculations on molecular and condensed-phase chemical reactions and other processes. entos focuses on multiscale embedding methods that allow for accurate simulation of a small, chemically important region, in a larger, complex chemical environment. '
EPIC'Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data. URL: https://gfellerlab.shinyapps.io/EPIC_1-1'
ESMF'The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. URL: https://www.earthsystemcog.org/projects/esmf/'
eSpeak-NG' The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington. URL: https://github.com/espeak-ng/espeak-ng'
Essentia'Open-source library and tools for audio and music analysis, description and synthesis URL: https://essentia.upf.edu'
eta' ETA Progress bar for command-line utilities'
ETE'A Python framework for the analysis and visualization of trees URL: http://etetoolkit.org'
ETSF_IO'A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. '
eudev' eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.'
Exonerate' 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 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) URL: https://libexpat.github.io'
expect'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. URL: https://core.tcl.tk/expect/index'
Extrae'Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application. URL: http://www.bsc.es/computer-sciences/performance-tools'
Faber'Faber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail. URL: https://stefanseefeld.github.io/faber Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
FALCON'Falcon: a set of tools for fast aligning long reads for consensus and assembly'
FANN'Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks.'
fast5' A lightweight C-- library for accessing Oxford Nanopore Technologies sequencing data.'
FASTA'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. URL: http://fasta.bioch.virginia.edu'
FastaIndex'FastA index (.fai) handler compatible with samtools faidx'
FastANI'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. URL: https://www.iodbc.org/'
FastME'FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.'
fastp'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. URL: https://github.com/OpenGene/fastp'
FastQC'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. URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/'
FastQ_Screen'FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.'
fastq-tools'This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.'
FastRFS'Fast Robinson Foulds Supertrees URL: https://github.com/pranjalv123/FastRFS'
fastsimcoal2'fast sequential Markov coalescent simulation of genomic data under complex evolutionary models URL: http://cmpg.unibe.ch/software/fastsimcoal2/'
fastStructure' fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. URL: https://rajanil.github.io/fastStructure/'
FastTree'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. URL: http://www.microbesonline.org/fasttree/'
FastViromeExplorer'Identify the viruses/phages and their abundance in the viral metagenomics data. URL: https://code.vt.edu/saima5/FastViromeExplorer'
FASTX-Toolkit'The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.'
FDS'Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. URL: https://pages.nist.gov/fds-smv/'
FEMZIP-L'FEMZIP-L is a data compression software package for LS-DYNA result files'
Ferret'Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. URL: https://ferret.pmel.noaa.gov/Ferret/'
festival' University of Edinburgh's Festival Speech Synthesis Systems is a free software multi-lingual speech synthesis workbench that runs on multiple-platforms offering black box text to speech, as well as an open architecture for research in speech synthesis. It designed as a component of large speech technology systems. URL: ['http://festvox.org/festival/']'
FFC'The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms.'
FFmpeg'A complete, cross-platform solution to record, convert and stream audio and video. URL: https://www.ffmpeg.org/'
FFTW'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. URL: http://www.fftw.org'
FIAT'The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.'
FigTree' FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures URL: http://tree.bio.ed.ac.uk/software/figtree/'
FigureGen' FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps. URL: https://ccht.ccee.ncsu.edu/category/software/figuregen/'
Fiji'Fiji image processing package'
file'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. URL: https://www.darwinsys.com/file/'
fineRADstructure'A package for population structure inference from RAD-seq data'
Fiona'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. URL: https://github.com/Toblerity/Fiona'
Firefox'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. URL: https://www.mozilla.org/en-US/firefox/new/'
FLAIR'FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads. URL: https://github.com/BrooksLabUCSC/flair'
FLANN'FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces.'
FLASH'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.'
Flask'" 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. URL: https://www.palletsprojects.com/p/flask/'
flatbuffers'FlatBuffers: Memory Efficient Serialization Library URL: https://github.com/google/flatbuffers/'
flatbuffers-python'Python Flatbuffers runtime library. URL: https://github.com/google/flatbuffers/'
flex' 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. URL: http://flex.sourceforge.net/'
FlexiDot' Highly customizable, ambiguity-aware dotplots for visual sequence analyses URL: https://github.com/molbio-dresden/flexidot'
Flink'Apache Flink is a framework and distributed processing engine for stateful computations over unbounded and bounded data streams. Flink has been designed to run in all common cluster environments, perform computations at in-memory speed and at any scale. URL: https://flink.apache.org/'
FLTK'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. URL: https://www.fltk.org'
Flye'Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. URL: https://github.com/fenderglass/Flye'
FMILibrary'FMI library is intended as a foundation for applications interfacing FMUs (Functional Mockup Units) that follow FMI Standard. This version of the library supports FMI 1.0 and FMI2.0. See http://www.fmi-standard.org/'
fmt'fmt (formerly cppformat) is an open-source formatting library.'
fontconfig' Fontconfig is a library designed to provide system-wide font configuration, customization and application access. URL: https://www.freedesktop.org/wiki/Software/fontconfig/'
foss'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. URL: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain'
fosscuda'GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. URL: (none)'
FoX'FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development.'
FragGeneScan'FragGeneScan is an application for finding (fragmented) genes in short reads. URL: https://omics.informatics.indiana.edu/FragGeneScan/'
FRANz'A fast and flexible parentage inference program for natural populations.'
FreeBayes'freebayes is a Bayesian genetic variant detector designed to find small polymorphisms URL: https://github.com/ekg/freebayes'
freeglut'freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. URL: http://freeglut.sourceforge.net/'
FreeImage'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. URL: http://freeimage.sourceforge.net'
FreeSASA'FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA). URL: https://freesasa.github.io'
freetype' 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. URL: https://www.freetype.org'
FreeXL' FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. URL: https://www.gaia-gis.it/fossil/freexl/index'
FriBidi' The Free Implementation of the Unicode Bidirectional Algorithm. URL: https://github.com/fribidi/fribidi'
FSL'FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. URL: https://www.fmrib.ox.ac.uk/fsl/'
fsspec'A specification for pythonic filesystems. URL: https://pypi.python.org/pypi/fsspec/'
FTGL' FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. URL: http://ftgl.sourceforge.net/docs/html/'
FUSE'The reference implementation of the Linux FUSE (Filesystem in Userspace) interface'
FuSeq'FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data. URL: https://github.com/nghiavtr/FuSeq'
FusionCatcher'FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq/MiniSeq) from diseased samples. URL: https://github.com/ndaniel/fusioncatcher'
future'python-future is the missing compatibility layer between Python 2 and Python 3.'
fxtract'Extract sequences from a fastx (fasta or fastq) file given a subsequence.'
g2clib'Library contains GRIB2 encoder/decoder ('C' version).'
g2lib'Library contains GRIB2 encoder/decoder and search/indexing routines.'
g2log'g2log, efficient asynchronous logger using C--11 URL: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11'
Gaia'Gaia is a C-- library with python bindings which implements similarity measures and classifications on the results of audio analysis, and generates classification models that Essentia can use to compute high-level description of music. URL: https://github.com/MTG/gaia'
gap'GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.'
GapCloser'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.'
GARLI'GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms. URL: https://code.google.com/archive/p/garli/'
gatb-core' You can use the GATB-Core library to develop new NGS data analysis softwares. URL: https://gatb.inria.fr/software/gatb-core/'
GATE'GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography'
GATK'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. URL: https://www.broadinstitute.org/gatk/ Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
gawk'gawk: GNU awk'
gc' The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C-- new. URL: https://hboehm.info/gc/'
GCATemplates'GCATemplates is a collection of HPC template scripts for tools useful for bioinformatics tasks. '
GCC'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,...). URL: https://gcc.gnu.org/'
GCCcore'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,...). URL: https://gcc.gnu.org/'
gcccuda'GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. URL: (none)'
GConf'GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.'
GC-schnablelab'GC imputes missing and corrects wrong genotype calls in bi-parental populations for genetic map constructions. URL: https://github.com/freemao/schnablelab/wiki/GC'
Gctf'Gctf: real-time CTF determination and correction, Kai Zhang, 2016 URL: https://www.mrc-lmb.cam.ac.uk/kzhang/'
GD'GD.pm - Interface to Gd Graphics Library URL: https://github.com/lstein/Perl-GD'
GDAL'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. URL: https://www.gdal.org'
GDB'The GNU Project Debugger URL: https://www.gnu.org/software/gdb/gdb.html'
gdbgui'Browser-based frontend to gdb (gnu debugger). Add breakpoints, view the stack, visualize data structures, and more in C, C--, Go, Rust, and Fortran. Run gdbgui from the terminal and a new tab will open in your browser.'
gdc-client'The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.'
GDCHART'Easy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format. URL: http://users.fred.net/brv/chart'
GDCM'Grassroots DICOM: Cross-platform DICOM implementation URL: https://sourceforge.net/projects/gdcm'
GDGraph'GDGraph is a Perl package to generate charts'
Gdk-Pixbuf' 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. URL: https://developer.gnome.org/gdk-pixbuf/stable/'
GDRCopy'A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. URL: https://github.com/NVIDIA/gdrcopy'
Geant4' 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. URL: https://geant4.web.cern.ch/'
Geant4-data'Datasets for Geant4. URL: https://geant4.cern.ch/'
gearshifft'Benchmark Suite for Heterogenuous FFT Implementations'
GEMMA'Genome-wide Efficient Mixed Model Association URL: https://github.com/genetics-statistics/GEMMA'
GeneMark-ES' GeneMark-ES - Gene Prediction in Eukaryotes. Unsupervised training is an important feature of the GeneMark-ES algorithm that identifies protein coding genes in eukaryotic genomes. This is the only eukaryotic gene finder that can perform gene prediction without curated training sets. URL: http://exon.gatech.edu/gmes_instructions.html'
GeneMarkS'GeneMarkS - Gene Prediction in Prokaryotes. URL: http://exon.gatech.edu/GeneMark/genemarks.cgi'
gengetopt'Gengetopt is a tool to write command line option parsing code for C programs. URL: https://www.gnu.org/software/gengetopt/gengetopt.html'
GenomeTester4'A toolkit for performing set operations - union, intersection and complement - on k-mer lists.'
GenomeTools'A comprehensive software library for efficient processing of structured genome annotations. URL: http://genometools.org'
geocube'Tool to convert geopandas vector data into rasterized xarray data. URL: https://corteva.github.io/geocube/latest/'
geopandas'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. URL: https://github.com/geopandas/geopandas'
GEOS'GEOS (Geometry Engine - Open Source) is a C-- port of the Java Topology Suite (JTS) URL: https://trac.osgeo.org/geos'
Gerris'Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow'
gettext'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 URL: https://www.gnu.org/software/gettext/'
GffCompare'GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.'
gffread'GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. URL: https://github.com/gpertea/gffread'
gflags' 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. URL: https://github.com/gflags/gflags'
ggplot2https://github.com/hadley/ggplot2 'An Implementation of the Grammar of Graphics'
Ghostscript'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. URL: https://ghostscript.com'
giflib'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. URL: http://giflib.sourceforge.net/'
gifsicle'Gifsicle is a command-line tool for creating, editing, and getting information about GIF images and animations. Making a GIF animation with gifsicle is easy. URL: https://github.com/kohler/gifsicle'
GIMIC'The GIMIC program calculates magnetically induced currents in molecules. You need to provide this program with a density matrix in atomic-orbital (AO) basis and three (effective) magnetically perturbed AO density matrices in the proper format. Currently ACES2, Turbomole, G09, QChem, FERMION--, and LSDalton can produce these matrices.'
gimkl'GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL'
gimpi'GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.'
giolf'GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
git'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. URL: https://git-scm.com/'
git-lfs'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 URL: https://git-lfs.github.com'
GitPython' GitPython is a python library used to interact with Git repositories URL: https://github.com/gitpython-developers/GitPython'
Giza'Giza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices.'
GL2PS'GL2PS: an OpenGL to PostScript printing library URL: https://www.geuz.org/gl2ps/'
Glade'Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK- toolkit and the GNOME desktop environment. URL: https://glade.gnome.org/'
glew'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. URL: https://github.com/nigels-com/glew'
GLib'GLib is one of the base libraries of the GTK- project URL: https://www.gtk.org/'
glibc'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. URL: https://www.gnu.org/software/libc/'
GLibmm'GLib is one of the base libraries of the GTK- project'
GLIMMER'Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.'
GlimmerHMM'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'OpenGL Mathematics (GLM) is a header only C-- mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. URL: https://github.com/g-truc/glm'
GlobalArrays'Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model URL: https://hpc.pnl.gov/globalarrays'
Globus-CLI'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. URL: https://docs.globus.org/cli/ Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
glog'A C-- implementation of the Google logging module. URL: https://github.com/google/glog'
GLPK'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. URL: https://www.gnu.org/software/glpk/'
glue'An implementation of interpreted string literals'
GMAP-GSNAP'GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program URL: http://research-pub.gene.com/gmap/'
GMP' GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. URL: https://gmplib.org/'
gmpich'gcc and GFortran based compiler toolchain, including MPICH for MPI support.'
gmpolf'gcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
gmpy2'GMP/MPIR, MPFR, and MPC interface to Python 2.6- and 3.x URL: https://github.com/aleaxit/gmpy Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
gmsh'Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. URL: https://gmsh.info'
GMT'GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. URL: https://gmt.soest.hawaii.edu/'
gnuplot'Portable interactive, function plotting utility URL: https://gnuplot.sourceforge.net/'
Go'Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. URL: https://www.golang.org'
goatools' Python scripts to find enrichment of GO terms'
GObject-Introspection'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. URL: https://gi.readthedocs.io/en/latest/'
golf'GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW. URL: (none)'
gomkl'GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL URL: (none)'
gompi'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. URL: (none)'
gompic'GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. URL: (none)'
google-auth' This library simplifies using Google’s various server-to-server authentication mechanisms to access Google APIs. URL: https://pypi.python.org/pypi/google-auth/'
googletest'Google's framework for writing C-- tests on a variety of platforms URL: https://github.com/google/googletest'
goolfc'GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
GPAW'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. URL: https://wiki.fysik.dtu.dk/gpaw/'
GPAW-setups'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' 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. URL: https://www.gnu.org/software/gperf/'
gperftools'gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C-- with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. URL: https://github.com/gperftools/gperftools'
GPflow' GPflow is a package for building Gaussian process models in python using TensorFlow.'
gprMax' gprMax is open source software that simulates electromagnetic wave propagation. It uses Yee's algorithm to solve Maxwell’s equations in 3D using the Finite-Difference Time-Domain (FDTD) method.'
gpustat'dstat-like utilization monitor for NVIDIA GPUs URL: https://github.com/wookayin/gpustat'
Grace'Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. URL: https://plasma-gate.weizmann.ac.il/Grace/'
gradunwarp'Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original. URL: https://github.com/Washington-University/gradunwarp'
GraphicsMagick'GraphicsMagick is the swiss army knife of image processing. URL: https://www.graphicsmagick.org/'
GraphMap2'A highly sensitive and accurate mapper for long, error-prone reads URL: https://github.com/lbcb-sci/graphmap2'
graph-tool'Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C--, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C-- library. URL: https://graph-tool.skewed.de/'
Graphviz'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. URL: https://www.graphviz.org/'
GRASP'The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms. URL: https://compas.github.io/grasp/'
GRASS'The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization URL: https://grass.osgeo.org'
gretl'A cross-platform software package for econometric analysis URL: http://gretl.sourceforge.net'
grib_api' The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages.'
GROMACS'Description: 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 an MPI, PLUMED, and GPU enabled build (gmx_mpi). URL: http://www.gromacs.org'
GromacsWrapper' GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts. URL: https://gromacswrapper.readthedocs.org'
GSL'The GNU Scientific Library (GSL) is a numerical library for C and C-- programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. URL: https://www.gnu.org/software/gsl/'
gSOAP'The gSOAP toolkit is a C and C-- software development toolkit for SOAP and REST XML Web services and generic C/C-- XML data bindings. The toolkit analyzes WSDLs and XML schemas (separately or as a combined set) and maps the XML schema types and the SOAP/REST XML messaging protocols to easy-to-use and efficient C and C-- code. It also supports exposing (legacy) C and C-- applications as XML Web services by auto-generating XML serialization code and WSDL specifications. Or you can simply use it to automatically convert XML to/from C and C-- data. The toolkit supports options to generate pure ANSI C or C-- with or without STL. URL: https://www.cs.fsu.edu/~engelen/soap.html'
gsport'GSPORT command-line tool for accessing GenomeScan Customer Portal URL: https://github.com/genomescan/gsport'
GST-plugins-base'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. URL: https://gstreamer.freedesktop.org/'
GStreamer'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. URL: https://gstreamer.freedesktop.org/'
gtable'Arrange 'Grobs' in Tables'
GTDB-Tk'A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. URL: https://github.com/Ecogenomics/GTDBTk'
gtest'Google's framework for writing C-- tests on a variety of platforms URL: https://github.com/google/googletest'
GTK+'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. URL: https://developer.gnome.org/gtk3/stable/'
Gtkmm' The Gtkmm package provides a C-- interface to GTK- 3. '
GtkSourceView' GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK- widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor. URL: https://wiki.gnome.org/Projects/GtkSourceView'
GTS'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.'
guenomu'guenomu is a software written in C that estimates the species tree for a given set of gene families. URL: https://bitbucket.org/leomrtns/guenomu'
Guile' 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'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. URL: https://www.gurobi.com'
gzip'gzip (GNU zip) is a popular data compression program as a replacement for compress URL: https://www.gnu.org/software/gzip/'
h4toh5'The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects. URL: http://www.hdfgroup.org/h4toh5/'
h5py'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. URL: https://www.h5py.org/'
Hadoop'Hadoop MapReduce by Cloudera URL: https://archive.cloudera.com/cdh5/cdh/5/'
HarfBuzz'HarfBuzz is an OpenType text shaping engine. URL: https://www.freedesktop.org/wiki/Software/HarfBuzz'
Harminv'Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. URL: https://github.com/stevengj/harminv'
harmony'Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. URL: https://portals.broadinstitute.org/harmony'
HDDM'HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC). URL: http://ski.clps.brown.edu/hddm_docs'
HDF' HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. URL: https://www.hdfgroup.org/products/hdf4/'
HDF5'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. URL: https://portal.hdfgroup.org/display/support'
hdf5storage'This Python package provides high level utilities to read/write a variety of Python types to/from HDF5 (Heirarchal Data Format) formatted files. This package also provides support for MATLAB MAT v7.3 formatted files, which are just HDF5 files with a different extension and some extra meta-data. All of this is done without pickling data. Pickling is bad for security because it allows arbitrary code to be executed in the interpreter. One wants to be able to read possibly HDF5 and MAT files from untrusted sources, so pickling is avoided in this package. URL: https://pythonhosted.org/hdf5storage/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
HDF-EOS' HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. URL: http://hdfeos.org/'
HDF-EOS5'HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. URL: https://hdfeos.org/'
HEALPix'Hierarchical Equal Area isoLatitude Pixelation of a sphere. URL: http://healpix.sourceforge.net/'
HeFFTe'Highly Efficient FFT for Exascale (HeFFTe) library URL: https://icl.utk.edu/fft'
Hello' The GNU Hello program produces a familiar, friendly greeting. Yes, this is another implementation of the classic program that prints "Hello, world!" when you run it. However, unlike the minimal version often seen, GNU Hello processes its argument list to modify its behavior, supports greetings in many languages, and so on. URL: https://www.gnu.org/software/hello/'
help2man'help2man produces simple manual pages from the '--help' and '--version' output of other commands. URL: https://www.gnu.org/software/help2man/'
HERA'HERA is a local assembly tool using assembled contigs and self-corrected long reads as input. HERA is highly efficient using SMS data to resolve repeats, which enables the assembly of highly contiguous genomes. URL: https://github.com/liangclab/HERA'
HH-suite'HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. URL: https://github.com/soedinglab/hh-suite'
hierfstat'Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy. URL: https://cran.r-project.org/package=hierfstat'
HISAT2'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). URL: https://ccb.jhu.edu/software/hisat2/index.shtml'
HLAminer' HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads. URL: http://www.bcgsc.ca/platform/bioinfo/software/hlaminer'
HMMER'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. URL: http://hmmer.org/'
HMMER2'HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. URL: http://hmmer.org'
Homer'HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.'
Horovod'Horovod is a distributed training framework for TensorFlow. URL: https://github.com/uber/horovod'
horton'HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost. Although HORTON is primarily designed to be a quantum-chemistry program, it can perform computations involving model Hamiltonians, and could be extended for computations in nuclear physics. URL: https://theochem.github.io/horton'
HPCG'The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark. URL: https://software.sandia.gov/hpcg'
HPL'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. URL: https://www.netlib.org/benchmark/hpl/'
htop'An interactive process viewer for Unix'
HTSeq'HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. URL: https://github.com/simon-anders/htseq'
HTSlib' A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix URL: http://www.htslib.org/'
hunspell'Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.'
hwloc' 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. URL: https://www.open-mpi.org/projects/hwloc/'
hyperopt'Distributed Asynchronous Hyperparameter Optimization in Python URL: https://github.com/hyperopt/hyperopt'
Hyperworks'Computer-aided engineering simulator.'
HyPhy'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 URL: https://veg.github.io/hyphy-site/'
hypothesis'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. URL: https://github.com/HypothesisWorks/hypothesis'
Hypre'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. URL: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods'
ICA-AROMA'ICA-AROMA (i.e. 'ICA-based Automatic Removal Of Motion Artifacts') concerns a data-driven method to identify and remove motion-related independent components from fMRI data.'
icc'Intel C and C-- compilers URL: http://software.intel.com/en-us/intel-compilers/'
iccifort'Intel C, C-- & Fortran compilers URL: https://software.intel.com/en-us/intel-compilers/'
iccifortcuda'Intel C, C-- & Fortran compilers with CUDA toolkit URL: (none)'
IceT' The Image Composition Engine for Tiles (IceT) is a high-performance sort-last parallel rendering library.'
ichorCNA'ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing URL: https://github.com/broadinstitute/ichorCNA/wiki'
iCount' iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.'
ICU'ICU is a mature, widely used set of C/C-- and Java libraries providing Unicode and Globalization support for software applications. URL: https://icu-project.org/'
Icy'Icy is an open community platform for bioimage informatics.'
IDBA-UD' 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. URL: https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/'
IDL' EXELIS IDL is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy, atmospheric physics and medical imaging. URL: http://www.exelisvis.com/ProductsServices/IDL.aspx'
IDLENVI' EXELIS IDL is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy, atmospheric physics and medical imaging. '
ifort'Intel Fortran compiler URL: http://software.intel.com/en-us/intel-compilers/'
IgBLAST'IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. URL: https://ncbi.github.io/igblast'
igraph'igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C--. URL: https://igraph.org'
IGV'The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. URL: https://www.broadinstitute.org/igv/home'
igv-reports'Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol. URL: https://github.com/igvteam/igv-reports'
IGVTools' This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline. URL: https://software.broadinstitute.org/software/igv/igvtools'
iimpi'Intel C/C-- and Fortran compilers, alongside Intel MPI. URL: https://software.intel.com/parallel-studio-xe'
iimpic'Intel C/C-- and Fortran compilers, alongside Intel MPI and CUDA. URL: (none)'
ILAMB' The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns to reduce uncertainties associated with key land surface processes. URL: https://www.ilamb.org/'
imageio'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. URL: https://imageio.github.io'
ImageJ'Image Processing and Analysis in Java URL: https://imagej.nih.gov/ij'
ImageMagick'ImageMagick is a software suite to create, edit, compose, or convert bitmap images URL: https://www.imagemagick.org/'
IMB'The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes URL: https://software.intel.com/en-us/articles/intel-mpi-benchmarks'
imbalanced-learn'imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.'
imgaug' This python library helps you with augmenting images for your machine learning projects. It converts a set of input images into a new, much larger set of slightly altered images. URL: https://imgaug.readthedocs.io/en/latest/'
imkl'Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. URL: https://software.intel.com/mkl'
impi'Intel MPI Library, compatible with MPICH ABI URL: https://software.intel.com/en-us/intel-mpi-library/'
IMSindel'An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis. URL: https://github.com/NCGG-MGC/IMSindel'
Inelastica'Python package for eigenchannels, vibrations and inelastic electron transport based on SIESTA/TranSIESTA DFT.'
Infernal'Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.'
Infomap'Multi-level network clustering based on the Map equation. URL: https://www.mapequation.org/code.html#Linux'
inputproto'X.org InputProto protocol headers.'
IntaRNA'Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites'
INTEGRATE' INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on Burrow-Wheeler transform. URL: https://sourceforge.net/p/integrate-fusion/wiki/Home/'
intel'Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). URL: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain'
intelcuda'Intel Cluster Toolkit Compiler Edition provides Intel C/C-- and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit URL: (none)'
IntelPython' Intel® Distribution for Python. Powered by Anaconda. Accelerating Python- performance on modern architectures from Intel.'
InterProScan' InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. URL: http://www.ebi.ac.uk/interpro'
intltool'intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. URL: https://freedesktop.org/wiki/Software/intltool/'
ioapi'The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) and model coupling (using PVM mailboxes). It is the standard data access library for both the NCSC/CMAS's EDSS project and EPA's Models-3, CMAQ, and SMOKE, as well as various other atmospheric and hydrological modeling systems. URL: https://www.cmascenter.org/ioapi/'
iomkl'Intel Cluster Toolchain Compiler Edition provides Intel C/C-- and Fortran compilers, Intel MKL & OpenMPI. URL: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
iompi'Intel C/C-- and Fortran compilers, alongside Open MPI. URL: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
IOR' The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. URL: https://github.com/IOR-LANL/ior'
IPM' IPM is a portable profiling infrastructure for parallel codes. It provides a low-overhead profile of application performance and resource utilization in a parallel program. Communication, computation, and IO are the primary focus. URL: https://github.com/nerscadmin/IPM'
Ipopt'Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization. URL: https://coin-or.github.io/Ipopt'
ipyparallel'ipyparallel is a Python package and collection of CLI scripts for controlling clusters for Jupyter'
IPython'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. URL: https://ipython.org/index.html'
IQ-TREE'Efficient phylogenomic software by maximum likelihood URL: http://www.iqtree.org/'
IRkernel'The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network. URL: https://irkernel.github.io'
isPcr' Command line program that builds its own index (rather than relying on gfServer) to do PCR. This uses a lot of memory and is best done one chromosome at a time in batch mode, ideally on a cluster of machines. URL: https://users.soe.ucsc.edu/~kent'
ITK'Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. URL: https://itk.org'
itpp'IT-- is a C-- library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications. URL: https://sourceforge.net/projects/itpp/'
itsdangerous' Various helpers to pass trusted data to untrusted environments and back.'
ITSTool'ITS Tool allows you to translate your XML documents with PO files, using rules from the W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages. URL: https://itstool.org/'
JAGS'JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation URL: http://mcmc-jags.sourceforge.net/'
JasPer' 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. URL: https://www.ece.uvic.ca/~frodo/jasper/'
Java'Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. URL: https://openjdk.java.net'
JavaCyc'Javacyc is a java class for accessing internal Pathway-Tools functions. URL: https://pmn.dpb.carnegiescience.edu/'
jbigkit'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. URL: https://www.cl.cam.ac.uk/~mgk25/jbigkit/'
JBIG-KIT' JBIG-KIT provides a portable library of compression and decompression functions with a documented interface that you can include very easily into your image or document processing software.'
JBrowse'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.'
JDK' Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.'
Jellyfish'Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. URL: http://www.genome.umd.edu/jellyfish.html'
jemalloc'jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. URL: http://jemalloc.net'
Jinja2' Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.'
JiTCODE'Just-in-time compilation for ordinary/delay/stochastic differential equations (DDEs) URL: https://jitcde-common.readthedocs.io'
joypy'Joyplots in Python with matplotlib & pandas URL: https://github.com/sbebo/joypy'
json2html' Python wrapper to convert JSON into a human readable HTML Table representation.'
JsonCpp' 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. URL: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html'
JUBE'The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results. URL: https://www.fz-juelich.de/jsc/jube'
Judy'A C library that implements a dynamic array. URL: http://judy.sourceforge.net/'
Juicer'Juicer is a one-click pipeline for processing terabase scale Hi-C datasets.'
Juicer_tools'Tools for use with the Juicer application.'
Julia'Julia is a high-level, high-performance dynamic programming language for numerical computing URL: https://julialang.org'
Julia_tamu'Julia is a high-level, high-performance dynamic programming language for numerical computing..'
JupyterHub'JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs. URL: https://jupyter.org'
JupyterLab'JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook. URL: https://jupyter.org/'
Kaiju'Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments URL: http://kaiju.binf.ku.dk/'
kallisto'kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. URL: https://pachterlab.github.io/kallisto/'
KAT'The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra. URL: https://www.earlham.ac.uk/kat-tools'
kbproto'X.org KBProto protocol headers.'
kedro' Kedro is an open-source Python framework that applies software engineering best-practice to data and machine-learning pipelines. URL: https://github.com/quantumblacklabs/kedro'
Kent_tools'Kent tools: collection of tools used by the UCSC genome browser. URL: http://genome.cse.ucsc.edu/'
Keras'Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. URL: https://keras.io/'
kim-api'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. URL: https://openkim.org/'
kma'KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. URL: https://bitbucket.org/genomicepidemiology/kma'
KMC'KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.'
Knitro' 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.'
KNL'Knights Landing optimized packages for terra.hprc.tamu.edu'
Kokkos' Kokkos implements a programming model in C-- for writing performance portable applications targeting all major HPC platforms.'
KorfLab-Perl_utils'Miscellaneous Perl scripts and modules used by people in the Korf lab. URL: http://korflab.ucdavis.edu/'
Krait'Microsatellite investigation and primer design URL: https://github.com/lmdu/krait'
Kraken'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. URL: https://ccb.jhu.edu/software/kraken/'
Kraken2'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. URL: http://www.ccb.jhu.edu/software/kraken2/'
Kratos'Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software.'
KronaTools'Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.'
kwant'Kwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport. URL: https://kwant-project.org/'
KyotoCabinet'Kyoto Cabinet is a library of routines for managing a database. URL: https://fallabs.com/kyotocabinet'
labeling'Axis Labeling'
LAME'LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. URL: http://lame.sourceforge.net/'
LAMMPS'LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. '
LAPACK'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. URL: http://www.netlib.org/lapack/'
LAST'LAST finds similar regions between sequences. URL: http://last.cbrc.jp/'
LASTZ' 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. URL: https://www.bx.psu.edu/~rsharris/lastz/'
LaTeX'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. '
LATTE' Open source density functional tight binding molecular dynamics.'
lavaan'lavaan is a free, open source R package for latent variable analysis URL: http://lavaan.org'
LCov'LCOV - the LTP GCOV extension'
leidenalg'Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python. URL: https://github.com/vtraag/leidenalg'
Leptonica'Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.'
LevelDB'LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.'
lftp'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.'
libaio'Asynchronous input/output library that uses the kernels native interface. URL: https://pagure.io/libaio'
libarchive' Multi-format archive and compression library URL: https://www.libarchive.org/'
libart' Graphics routines used by the GnomeCanvas widget and some other applications. libart renders vector paths and the like. URL: http://www.gnome.org/'
libav' Libav is a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts.'
libBigWig'A C library for handling bigWig files URL: https://github.com/dpryan79/libBigWig'
libcerf' 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. URL: https://jugit.fz-juelich.de/mlz/libcerf'
libcircle' An API to provide an efficient distributed queue on a cluster. libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization. URL: https://github.com/hpc/libcircle/'
libconfig'Libconfig is a simple library for processing structured configuration files'
libctl'libctl is a free Guile-based library implementing flexible control files for scientific simulations. URL: http://ab-initio.mit.edu/libctl'
libdap'A C-- SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. URL: https://www.opendap.org/software/libdap'
libdrm'Direct Rendering Manager runtime library. URL: https://dri.freedesktop.org'
libdwarf'The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information)) URL: http://www.prevanders.net/dwarf.html'
libedit' This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline.'
libelf'libelf is a free ELF object file access library URL: http://www.mr511.de/software/english.html'
libepoxy'Epoxy is a library for handling OpenGL function pointer management for you URL: https://github.com/anholt/libepoxy'
libevent' 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. URL: https://libevent.org/'
libfabric' 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. URL: https://ofiwg.github.io/libfabric/'
libffcall' GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters URL: https://www.gnu.org/software/libffcall/'
libffi'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. URL: https://sourceware.org/libffi/'
libFLAME'libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK. URL: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame'
libgcrypt'Libgpg-error is a small library that defines common error values for all GnuPG components. URL: https://gnupg.org/related_software/libgcrypt/index.html'
libgd'GD is an open source code library for the dynamic creation of images by programmers. URL: https://libgd.github.io/'
libgeotiff'Library for reading and writing coordinate system information from/to GeoTIFF files URL: https://directory.fsf.org/wiki/Libgeotiff'
libgit2' libgit2 is a portable, pure C implementation of the Git core methods provided as a linkable library with a solid API, allowing to build Git functionality into your application. URL: https://github.com/libgit2/libgit2'
libglade' Libglade is a library for constructing user interfaces dynamically from XML descriptions.'
libGLU'The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. URL: https://mesa.freedesktop.org/archive/glu/'
libglvnd'libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. URL: https://gitlab.freedesktop.org/glvnd/libglvnd'
libgnomecanvas' The canvas widget allows you to create custom displays using stock items such as circles, lines, text, and so on. It was originally a port of the Tk canvas widget but has evolved quite a bit over time.'
libgpg-error'Libgpg-error is a small library that defines common error values for all GnuPG components. URL: https://gnupg.org/related_software/libgpg-error/index.html'
libgpuarray' Library to manipulate tensors on the GPU.'
libGridXC'A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. URL: https://launchpad.net/libgridxc'
libgtextutils'ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream'
libharu'libHaru is a free, cross platform, open source library for generating PDF files.'
libICE' X Inter-Client Exchange library for freedesktop.org'
libiconv'Libiconv converts from one character encoding to another through Unicode conversion URL: https://www.gnu.org/software/libiconv'
libidn'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. URL: http://www.gnu.org/software/libidn'
Libint'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. URL: https://github.com/evaleev/libint'
libjpeg-turbo' 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. URL: https://sourceforge.net/projects/libjpeg-turbo/'
libmatheval'GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. URL: https://www.gnu.org/software/libmatheval/'
libmaus2'libmaus2 is a collection of data structures and algorithms.'
libMemcached'libMemcached is an open source C/C-- client library and tools for the memcached server (http://danga.com/memcached). It has been designed to be light on memory usage, thread safe, and provide full access to server side methods.'
libMesh' The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. NOTE: This module has been specifically configured for use with MOOSE (http://mooseframework.org/). URL: http://libmesh.github.io/'
libmicrohttpd' GNU libmicrohttpd is a small C library that is supposed to make it easy to run an HTTP server as part of another application. URL: https://www.gnu.org/software/libmicrohttpd/'
libobjcryst'ObjCryst-- is Object-Oriented Crystallographic Library for C-- URL: https://github.com/diffpy/libobjcryst'
libosmium'A fast and flexible C-- library for working with OpenStreetMap data. The Osmium Library has extensive support for all types of OSM entities: nodes, ways, relations, and changesets. It allows reading from and writing to OSM files in XML and PBF formats, including change files and full history files. Osmium can store OSM data in memory and on disk in various formats and using various indexes. Its easy to use handler interface allows you to quickly write data filtering and conversion functions. Osmium can create WKT, WKB, OGR, GEOS and GeoJSON geometries for easy conversion into many GIS formats and it can assemble multipolygons from ways and relations. URL: https://osmcode.org/libosmium/'
libpciaccess'Generic PCI access library. URL: https://cgit.freedesktop.org/xorg/lib/libpciaccess/'
libpng'libpng is the official PNG reference library URL: http://www.libpng.org/pub/png/libpng.html'
libpsl'C library for the Public Suffix List URL: https://rockdaboot.github.io/libpsl'
libpthread-stubs' 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.'
libQGLViewer'libQGLViewer is a C-- library based on Qt that eases the creation of OpenGL 3D viewers.'
libreadline' 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. URL: https://tiswww.case.edu/php/chet/readline/rltop.html'
libsamplerate'Secret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio. URL: http://www.mega-nerd.com/libsamplerate'
libsigc++'The libsigc-- package implements a typesafe callback system for standard C--. URL: https://libsigcplusplus.github.io/libsigcplusplus/'
libsigsegv'GNU libsigsegv is a library for handling page faults in user mode. URL: https://www.gnu.org/software/libsigsegv/'
libsndfile'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. URL: http://www.mega-nerd.com/libsndfile'
libsodium' Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. URL: https://doc.libsodium.org/'
LibSoup'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. URL: https://wiki.gnome.org/Projects/libsoup'
libspatialindex'C-- implementation of R--tree, an MVR-tree and a TPR-tree with C API'
libspatialite'SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.'
LIBSVM'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.'
libtar'C library for manipulating POSIX tar files'
libtasn1'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. URL: https://www.gnu.org/software/libtasn1/'
LibTIFF'tiff: Library and tools for reading and writing TIFF data files URL: https://libtiff.maptools.org/'
libtirpc'Libtirpc is a port of Suns Transport-Independent RPC library to Linux. URL: https://sourceforge.net/projects/libtirpc/'
libtool' GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. URL: https://www.gnu.org/software/libtool'
libunistring' This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. URL: https://www.gnu.org/software/libunistring/'
libunwind'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 URL: https://www.nongnu.org/libunwind/'
LibUUID'Portable uuid C library URL: http://sourceforge.net/projects/libuuid/'
libvdwxc'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. URL: https://libvdwxc.org'
libwebp'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. URL: https://developers.google.com/speed/webp/'
libX11'X11 client-side library'
libXau'The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.'
libxc'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. URL: https://www.tddft.org/programs/libxc'
libxcb'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'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.'
libxml++'libxml-- is a C-- wrapper for the libxml XML parser library. URL: http://libxmlplusplus.sourceforge.net'
libxml2' Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). URL: http://xmlsoft.org/'
libxml2-python' Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). This is the Python binding. URL: http://xmlsoft.org/'
libXp'libXp provides the X print library.'
libxslt'Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). URL: http://xmlsoft.org/'
libxsmm'LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). URL: https://github.com/hfp/libxsmm'
libyaml'LibYAML is a YAML parser and emitter written in C. URL: https://pyyaml.org/wiki/LibYAML'
libzeep'Libzeep was originally developed to make it easy to create SOAP servers. URL: https://github.com/mhekkel/libzeep'
lifelines'lifelines is a pure Python implementation of the best parts of survival analysis URL: https://lifelines.readthedocs.io'
LIGGGHTS' LIGGGHTS® is an Open Source Discrete Element Method Particle Simulation Software. It can be used for the simulation of particulate materials, and aims to for applications it to industrial problems '
LIGGGHTS-PUBLIC' LIGGGHTS® is an Open Source Discrete Element Method Particle Simulation Software. It can be used for the simulation of particulate materials, and aims to for applications it to industrial problems '
LIGGGHTS-PUBLIC-JKR' LIGGGHTS® is an Open Source Discrete Element Method Particle Simulation Software. It can be used for the simulation of particulate materials, and aims to for applications it to industrial problems URL: https://www.cfdem.com/'
LIGGGHTS-WITH-BONDS'LIGGGHTS® DEM software with Bonds enabled.'
Lighter'Fast and memory-efficient sequencing error corrector'
likwid' 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. URL: https://github.com/RRZE-HPC/likwid'
limix-bgen'A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. URL: https://github.com/limix/bgen'
lis' 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. URL: https://www.ssisc.org/lis/'
LittleCMS' Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. URL: http://www.littlecms.com/'
LLVM'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. URL: https://llvm.org/'
llvmlite'A lightweight LLVM python binding for writing JIT compilers URL: https://github.com/numba/llvmlite'
LMDB'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. URL: https://symas.com/lmdb'
LMfit'Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python URL: https://lmfit.github.io/lmfit-py'
LocARNA'LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure.'
LoFreq'Fast and sensitive variant calling from next-gen sequencing data'
Loki' Loki is a C-- library of designs, containing flexible implementations of common design patterns and idioms. '
LongQC'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. URL: https://github.com/yfukasawa/LongQC'
LoRDEC' LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. URL: http://www.atgc-montpellier.fr/lordec'
lpsolve'Mixed Integer Linear Programming (MILP) solver'
lrslib'lrslib is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems'
LSC' LSC is a pure implementation of the long read error correction algorithm. Long reads and high-quality short reads are homopolyer-compressed. Then, compressed short reads are mapped to compressed long reads with Bowtie2. Then the concensus sequences for short reads will replace the mapped regions in the long reads.'
LS-DYNA'LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems.'
LS-OPT'LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA.'
LS-PREPOST'LS-PREPOST is an advanced pre and post-processor that is delivered free with LS-DYNA.'
LS-TASC'LS-TaSC is a Topology and Shape Computation tool. Developed for engineering analysts who need to optimize structures.'
LtrDetector'A modern tool-suite for detectinglong terminal repeat retrotransposons de-novo onthe genomic scale URL: https://github.com/TulsaBioinformaticsToolsmith/LtrDetector'
Lua'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. URL: https://www.lua.org/'
LuaJIT' LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language.'
LUSCUS'Luscus is the program for graphical display and editing of molecular systems. URL: https://sourceforge.net/projects/luscus/'
lwgrp' The Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups URL: https://github.com/llnl/lwgrp'
lxml'The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. URL: https://lxml.de/ Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
lz4'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. URL: https://lz4.github.io/lz4/'
LZO'Portable lossless data compression library'
M4' 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. URL: http://www.gnu.org/software/m4/m4.html'
MACS2'Model Based Analysis for ChIP-Seq data URL: https://github.com/taoliu/MACS/'
maeparser'maeparser is a parser for Schrodinger Maestro files. URL: https://github.com/schrodinger/maeparser'
MAFFT'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. URL: https://mafft.cbrc.jp/alignment/software/source.html'
Magics' Magics is the latest generation of the ECMWF's meteorological plotting software and can be either accessed directly through its Python or Fortran interfaces or by using Metview.'
magma'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. URL: https://icl.cs.utk.edu/magma/'
MagresPython' MagresPython is a Python library for parsing the CCP-NC ab-initio magnetic resonance file format. This is used in the latest version of the CASTEP and Quantum ESPRESSO (PWSCF) codes. '
magrittr'A Forward-Pipe Operator for R'
make'GNU version of make utility URL: https://www.gnu.org/software/make/make.html'
makedepend'The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. URL: https://linux.die.net/man/1/makedepend'
MAKER'A portable and easily configurable genome annotation pipeline. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. URL: http://www.yandell-lab.org/software/maker.html'
Mako'A super-fast templating language that borrows the best ideas from the existing templating languages URL: https://www.makotemplates.org Compatible modules: Python/3.8.6-GCCcore-10.2.0 (default), Python/2.7.18-GCCcore-10.2.0'
manta' Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. URL: https://github.com/Illumina/manta'
MapSplice'MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.'
MariaDB'MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. URL: https://mariadb.org/'
MariaDB-connector-c'MariaDB Connector/C is used to connect applications developed in C/C-- to MariaDB and MySQL databases. URL: https://downloads.mariadb.org/connector-c/'
MarkupSafe'Python http for humans'
MARS'improving Multiple circular sequence Alignment using Refined Sequences URL: https://github.com/lorrainea/MARS'
Mash'Fast genome and metagenome distance estimation using MinHash'
MashMap' 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. URL: https://github.com/marbl/MashMap'
MASS'Support Functions and Datasets for Venables and Ripley's MASS'
MaSuRCA'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).'
matcaffe' matcaffe is the Matlab interface of caffe. Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by Berkeley AI Research (BAIR) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.'
Math-Derivative' Math::Derivative - Numeric 1st and 2nd order differentiation URL: https://metacpan.org/pod/Math::Derivative'
MathGL'MathGL is ... a library for making high-quality scientific graphics under Linux and Windows; a library for the fast data plotting and data processing of large data arrays; a library for working in window and console modes and for easy embedding into other programs; a library with large and growing set of graphics. '
Math-Spline' Math::Spline - Cubic Spline Interpolation of data URL: https://metacpan.org/pod/Math::Spline'
Math-Utils' Math::Utils - Useful mathematical functions not in Perl. URL: https://metacpan.org/pod/Math::Utils'
MATIO'matio is an C library for reading and writing Matlab MAT files. URL: https://sourceforge.net/projects/matio/'
Matlab'A numerical computing environment and fourth-generation programming language.'
Matlab-MCR'Sets up the runtime environment for standalone Matlab applications (generated using Matlab Application compiler).'
matplotlib'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. URL: https://matplotlib.org'
Mauve'Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. URL: http://darlinglab.org/mauve/mauve.html'
Maven'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. URL: https://maven.apache.org/index.html'
MavericK'MavericK is a program for inferring population structure on the basis of genetic information. The mixture modelling framework used by MavericK is identical to that used in the program STRUCTURE by Pritchard et al. (2000), which remains one of the most powerful and widely used programs in population genetics. URL: http://www.bobverity.com/home/maverick/what-is-maverick/'
mawk'mawk is an interpreter for the AWK Programming Language.'
MaxBin'MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. URL: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html'
Maxima' Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language.'
MBROLA'https://github.com/numediart/MBROLA-voices'] ' MBROLA is a speech synthesizer based on the concatenation of diphones. It takes a list of phonemes as input, together with prosodic information (duration of phonemes and a piecewise linear description of pitch), and produces speech samples on 16 bits (linear), at the sampling frequency of the diphone database. MBROLA voices project provides list of MBROLA speech synthesizer voices. It is intended to provide easier collaboration and automatic updates for individual users and packagers. URL: ['https://github.com/numediart/MBROLA', 'https://github.com/numediart/MBROLA-voices']'
mbuffer' mbuffer is a tool for buffering data streams with a large set of unique features. URL: https://www.maier-komor.de/mbuffer.html'
MCL'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. URL: https://micans.org/mcl/'
MCR'The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. URL: http://www.mathworks.com/products/compiler/mcr/'
MDAnalysis'MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. URL: https://www.mdanalysis.org/'
MDBM'MDBM is a super-fast memory-mapped key/value store URL: https://github.com/yahoo/mdbm'
MDSplus'MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data. URL: https://mdsplus.org'
MDSplus-Python'MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data. URL: https://mdsplus.org'
MDTraj'Read, write and analyze MD trajectories with only a few lines of Python code. URL: http://mdtraj.org'
medaka'medaka is a tool to create a consensus sequence of nanopore sequencing data.'
medImgProc'Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. URL: https://github.com/WeiXuanChan/motionSegmentation'
MedPy'MedPy is a library and script collection for medical image processing in Python, providing basic functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package. URL: https://pypi.org/project/MedPy/'
Meep'Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. URL: http://ab-initio.mit.edu/wiki/index.php/Meep'
MEGAHIT'An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph URL: https://github.com/voutcn/megahit Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
MEGASAT'MEGASAT is a software tool that can automatically infer genotypes from high-throughput microsatellite sequences. URL: https://github.com/beiko-lab/MEGASAT'
MEM'Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores. URL: https://github.com/cytolab/mem'
MEME'The MEME Suite allows you to: - discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, - search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, - compare a motif to all motifs in a database of motifs, - associate motifs with Gene Ontology terms via their putative target genes, and - analyse motif enrichment using SpaMo or CentriMo. URL: http://meme-suite.org'
memory-profiler'memory-profiler is a Python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption for python programs. URL: https://pypi.org/project/memory-profiler Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
Mesa'Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. URL: https://www.mesa3d.org/'
meshalyzer'Graphical program for display time dependent data on 3D finite elment meshes URL: https://git.opencarp.org/openCARP/meshalyzer'
meshio'meshio is a tool for reading/writing various mesh formats representing unstructured meshes'
meshtool'Meshtool is a comand-line tool written in C--. It is designed to apply various manipulations to volumetric meshes. URL: https://bitbucket.org/aneic/meshtool'
Meson'Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. URL: https://mesonbuild.com'
Mesquite'Mesh-Quality Improvement Library URL: https://software.sandia.gov/mesquite/'
MESS'Master Equation System Solver (MESS) URL: https://github.com/PACChem/MESS'
MetaBAT'An efficient tool for accurately reconstructing single genomes from complex microbial communities URL: https://bitbucket.org/berkeleylab/metabat Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
MetaboAnalystR'MetaboAnalystR contains the R functions and libraries underlying the popular MetaboAnalyst web server, including > 500 functions for metabolomic data analysis, visualization, and functional interpretation. URL: https://www.metaboanalyst.ca'
metaerg'MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline. URL: https://github.com/xiaoli-dong/metaerg'
MetaPhlAn2'MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.'
MetaPhysicL' Metaprogramming and operator-overloaded classes for numerical simulations URL: https://github.com/roystgnr/MetaPhysicL'
metaWRAP'MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. URL: https://github.com/bxlab/metaWRAP'
Metaxa2'Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically URL: https://microbiology.se/software/metaxa2/'
MethylDackel'A (mostly) universal methylation extractor for BS-seq experiments. URL: https://github.com/dpryan79/MethylDackel'
METIS'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.'
mhcflurry'MHCflurry implements class I peptide/MHC binding affinity prediction. By default it supports 112 MHC alleles using ensembles of allele-specific models. Pan-allele predictors supporting virtually any MHC allele of known sequence are available for testing (see below). MHCflurry runs on Python 2.7 and 3.4- using the keras neural network library. It exposes command-line and Python library interfaces. URL: https://github.com/openvax/mhcflurry'
MIGRATE-N' Migrate estimates population parameters, effective population sizes and migration rates of n populations, using genetic data. It uses a coalescent theory approach taking into account history of mutations and uncertainty of the genealogy. '
MINC'Medical Image NetCDF or MINC isn't netCDF.'
MinCED'Mining CRISPRs in Environmental Datasets URL: https://github.com/ctSkennerton/minced'
Miniconda2'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.'
Miniconda3'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. URL: https://docs.conda.io/en/latest/miniconda.html'
minieigen'A small wrapper for core parts of EIgen, c-- library for linear algebra.'
Minimac4'Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality.'
minimap2'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. URL: https://github.com/lh3/minimap2'
MinPath'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. URL: https://omics.informatics.indiana.edu/MinPath'
MIRA'MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). URL: https://sourceforge.net/p/mira-assembler/wiki/Home/'
miRDeep2' miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs '
misha'The misha package is intended to help users to efficiently analyze genomic data achieved from various experiments. URL: https://github.com/tanaylab/misha'
MITObim'The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads. URL: https://github.com/chrishah/MITObim'
MitoZ'MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. URL: https://github.com/linzhi2013/MitoZ'
MiXCR' MiXCR processes big immunome data from raw sequences to quantitated clonotypes URL: https://milaboratory.com/software/mixcr/'
mkl-dnn'Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)'
mkl-service'Python hooks for Intel(R) Math Kernel Library runtime control settings. URL: https://github.com/IntelPython/mkl-service Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
mlst'Scan contig files against traditional PubMLST typing schemes URL: https://github.com/tseemann/mlst'
MLxtend'Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks. URL: https://rasbt.github.io/mlxtend/'
MMseqs2'MMseqs2: ultra fast and sensitive search and clustering suite URL: https://mmseqs.com'
ModelTest-NG'ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments.'
Molden'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 is a Python library with many compoments that are useful to write molecular modeling programs. URL: https://molmod.github.io/molmod/'
Mono'An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. URL: https://www.mono-project.com/'
Monocle3' An analysis toolkit for single-cell RNA-seq. URL: https://cole-trapnell-lab.github.io/monocle3/'
MOOSE' The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory. It provides a high-level interface to some of the most sophisticated nonlinear solver technology on the planet.'
MoreRONN'MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography. URL: https://github.com/varun-ramraj/MoreRONN'
mosdepth'Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing'
Mothur'Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. URL: https://www.mothur.org/'
motif'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. URL: https://motif.ics.com/'
MotionCor2'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 URL: https://msg.ucsf.edu/'
motionSegmentation'Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. URL: https://github.com/WeiXuanChan/motionSegmentation'
MoviePy'MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects. URL: https://zulko.github.io/moviepy/'
MPC'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. URL: http://www.multiprecision.org/'
MPFR' The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. URL: https://www.mpfr.org'
mpi4py'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. URL: https://bitbucket.org/mpi4py/mpi4py Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
MPICH'MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). URL: http://www.mpich.org/'
mpifileutils' MPI-Based File Utilities For Distributed Systems URL: https://hpc.github.io/mpifileutils/'
mpiJava' mpiJava is an object-oriented Java interface to the standard Message Passing Interface (MPI). The interface was developed as part of the HPJava project, but mpiJava itself does not assume any special extensions to the Java language - it should be portable to any platform that provides compatible Java-development and native MPI environments.'
mpiP' mpiP is a lightweight profiling library for MPI applications. Because it only collects statistical information about MPI functions, mpiP generates considerably less overhead and much less data than tracing tools. All the information captured by mpiP is task-local. It only uses communication during report generation, typically at the end of the experiment, to merge results from all of the tasks into one output file. URL: https://mpip.sourceforge.net/'
mpmath'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. URL: http://mpmath.org/'
MRCPP'MultiResolution Computation Program Package URL: https://mrcpp.readthedocs.io'
MRtrix'MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. URL: http://www.brain.org.au/software/index.html#mrtrix'
msprime'msprime is a coalescent simulator and library for processing tree-based genetic data. URL: https://msprime.readthedocs.io'
MultiQC'Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. URL: https://multiqc.info'
Multiwfn'Multiwfn is an extremely powerful program for realizingi electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods. URL: http://sobereva.com/multiwfn/'
MUMmer' MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. URL: http://mummer.sourceforge.net/'
MUMPS'A parallel sparse direct solver URL: https://graal.ens-lyon.fr/MUMPS/'
munsell'Utilities for Using Munsell Colours'
muParser' muParser is an extensible high performance math expression parser library written in C--. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression.'
MuPeXI' MuPeXI: Mutant Peptide eXtractor and Informer. Given a list of somatic mutations (VCF file) as input, MuPeXI returns a table containing all mutated peptides (neo-peptides) of user-defined lengths, along with several pieces of information relevant for identifying which of these neo-peptides are likely to serve as neo-epitopes.'
MUSCLE'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. URL: https://drive5.com/muscle/'
MuSiC'Multi-subject Single Cell deconvolution (MuSiC) is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data. URL: https://github.com/xuranw/MuSiC'
MUST'MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers that want to develop correct MPI applications. This includes errors that already manifest – segmentation faults or incorrect results – as well as many errors that are not visible to the application developer or do not manifest on a certain system or MPI implementation. URL: https://hpc.rwth-aachen.de/must/'
MVAPICH2'The Open MPI Project is an open source MPI-2 implementation.'
mxml' Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries. URL: https://github.com/michaelrsweet/mxml/archive/v3.2.tar.gz'
mxmlplus'Mxml is a pure C library (yet having an object oriented layout) that is meant to help developers implementing XML file interpretation in their projects. URL: http://mxml.sourceforge.net'
myAnaconda2'A TAMU HPRC module to help users maintain their own virtual environments in $SCRATCH/myAnaconda2'
myAnaconda3'A TAMU HPRC module to help users maintain their own virtual environments in $SCRATCH/myAnaconda3'
myeb'User EasyBuild built modules in $SCRATCH/eb'
mygene'Python Client for MyGene.Info services. URL: https://github.com/biothings/mygene.py Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
myPython'A TAMU HPRC module to help users maintain their own virtual environments in $SCRATCH/myPython'
myR'A TAMU HPRC module to help users maintain their own R libraries in $SCRATCH/myR'
MySQL'MySQL is one of the world's most widely used open-source relational database management system (RDBMS).'
NAG'The worlds largest collection of robust, documented, tested and maintained numerical algorithms.'
NAMD'NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.'
NanoComp'Comparing runs of Oxford Nanopore sequencing data and alignments URL: https://github.com/wdecoster/NanoComp'
nanocompore'Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples URL: https://nanocompore.rna.rocks/'
NanoFilt'Filtering and trimming of Oxford Nanopore Sequencing data URL: https://github.com/wdecoster/nanofilt'
nanoget'Functions to extract information from Oxford Nanopore sequencing data and alignments URL: https://github.com/wdecoster/nanoget'
nanomath'A few simple math function for other Oxford Nanopore processing scripts URL: https://github.com/wdecoster/nanomath'
NanoPlot'Plotting suite for long read sequencing data and alignments URL: https://github.com/wdecoster/NanoPlot'
nanopolish'Software package for signal-level analysis of Oxford Nanopore sequencing data.'
NASM'NASM: General-purpose x86 assembler URL: https://www.nasm.us/'
ncbi-vdb'The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. URL: https://github.com/ncbi/ncbi-vdb'
NCCL'The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. URL: https://developer.nvidia.com/nccl'
ncdf4'ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files URL: https://cran.r-project.org/web/packages/ncdf4'
ncdu'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. URL: https://dev.yorhel.nl/ncdu'
NCL'NCL is an interpreted language designed specifically for scientific data analysis and visualization. URL: https://www.ncl.ucar.edu'
NCO'manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 URL: https://nco.sourceforge.net'
ncompress' Compress is a fast, simple LZW file compressor. Compress does not have the highest compression rate, but it is one of the fastest programs to compress data. Compress is the defacto standard in the UNIX community for compressing files.'
ncurses'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. URL: https://www.gnu.org/software/ncurses/'
ncview'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.'
neon' neon is an HTTP/1.1 and WebDAV client library, with a C interface. URL: https://github.com/notroj/neon'
Neper' Neper is a software package for polycrystal generation and meshing. It can deal with 2D and 3D polycrystals with very large numbers of grains. URL: http://www.neper.info/'
netCDF'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. URL: https://www.unidata.ucar.edu/software/netcdf/'
netcdf4-python'Python/numpy interface to netCDF. URL: https://unidata.github.io/netcdf4-python/'
netCDF-C++'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. URL: http://www.unidata.ucar.edu/software/netcdf/'
netCDF-C++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. URL: https://www.unidata.ucar.edu/software/netcdf/'
netCDF-Fortran'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. URL: https://www.unidata.ucar.edu/software/netcdf/'
NetPIPE'NetPIPE is a protocol independent communication performance benchmark that visually represents the network performance under a variety of conditions.'
nettle'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. URL: http://www.lysator.liu.se/~nisse/nettle/'
networkx'NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. URL: https://pypi.python.org/pypi/networkx'
NEURON'Empirically-based simulations of neurons and networks of neurons.'
Nextflow'Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data URL: https://www.nextflow.io'
NFFT'The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more dimensions, of arbitrary input size, and of complex data. URL: https://www-user.tu-chemnitz.de/~potts/nfft/'
nglview'IPython widget to interactively view molecular structures and trajectories. URL: https://github.com/arose/nglview'
NGS'NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. URL: https://github.com/ncbi/ngs'
NGSadmix'NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods.'
ngsLD'ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account. It does so by avoiding genotype calling and using genotype likelihoods or posterior probabilities. URL: https://github.com/fgvieira/ngsLD'
ngspice'Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. URL: https://ngspice.sourceforge.net'
NGS-Python'NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. URL: https://github.com/ncbi/ngs'
NGSUtils' NGSUtils is a suite of software tools for working with next-generation sequencing datasets'
NiBabel'NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. URL: https://nipy.github.io/nibabel'
NIfTI'Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format.'
nifti2dicom'Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS. URL: https://github.com/biolab-unige/nifti2dicom'
Nilearn'Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data. URL: http://nilearn.github.io/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
Nim'Nim is a systems and applications programming language. URL: https://nim-lang.org/'
NIMBLE'NIMBLE is a system for building and sharing analysis methods for statistical models, especially for hierarchical models and computationally-intensive methods. URL: https://r-nimble.org'
Ninja'Ninja is a small build system with a focus on speed. URL: https://ninja-build.org/'
Nipype'Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. URL: https://nipype.readthedocs.io'
NLMpy'NLMpy is a Python package for the creation of neutral landscape models that are widely used in the modelling of ecological patterns and processes across landscapes. URL: https://pypi.org/project/nlmpy'
NLopt' 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. URL: http://ab-initio.mit.edu/wiki/index.php/NLopt'
NLTK'NLTK is a leading platform for building Python programs to work with human language data. URL: https://www.nltk.org'
nodejs'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. URL: https://nodejs.org'
Normaliz'Normaliz is an open source tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones.'
nose-parameterized'Parameterized testing with any Python test framework.'
NOVOPlasty'NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. URL: https://github.com/ndierckx/NOVOPlasty'
NSPR'Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR'
NSS'Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS'
nsync'nsync is a C library that exports various synchronization primitives, such as mutexes URL: https://github.com/google/nsync'
ntHits'ntHits is a method for identifying repeats in high-throughput DNA sequencing data. URL: https://github.com/bcgsc/ntHits'
numactl' 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. URL: https://github.com/numactl/numactl'
numba'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. URL: https://numba.pydata.org/'
numexpr'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. URL: https://numexpr.readthedocs.io/en/latest/'
numpy'NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C-- and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. URL: http://www.numpy.org'
NVBIO'NVBIO is a library of reusable components designed by NVIDIA Corporation to accelerate bioinformatics applications using CUDA. It contains the nvBowtie and nvLighter applications.'
nvtop'htop-like GPU usage monitor URL: https://github.com/Syllo/nvtop'
NWChem'NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. URL: http://www.nwchem-sw.org'
NxTrim'NxTrim is a software to remove Nextera Mate Pair junction adapters and categorise reads according to the orientation implied by the adapter location.'
oauthlib' A generic, spec-compliant, thorough implementation of the OAuth request-signing logic for Python 2.7 and 3.4-. URL: https://pypi.org/project/oauthlib/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
OCaml'OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.'
occt'Open CASCADE Technology (OCCT) is an object-oriented C-- class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. URL: https://www.opencascade.com/'
Octave'GNU Octave is a high-level interpreted language, primarily intended for numerical computations. URL: https://www.gnu.org/software/octave/'
OligoArrayAux'OligoArrayAux is a subset of the UNAFold package for use with OligoArray. URL: http://unafold.rna.albany.edu/?q=DINAMelt/OligoArrayAux'
oneTBB'Official Threading Building Blocks (TBB) GitHub repository. 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. For Commercial Intel® TBB distribution, please see: https://software.intel.com/en-us/tbb URL: https://github.com/oneapi-src/oneTBB'
ont-fast5-api' Oxford Nanopore Technologies fast5 API software'
OOF2'OOF: Finite Element Analysis of Microstructures'
OOF3D'OOF: Finite Element Analysis of Microstructures'
OPARI2' OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. URL: https://www.score-p.org'
OpenAI-Gym'A toolkit for developing and comparing reinforcement learning algorithms. URL: https://gym.openai.com'
OpenBabel'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. URL: https://openbabel.org'
OpenBLAS'OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. URL: https://xianyi.github.com/OpenBLAS/'
openCARP'openCARP is an open cardiac electrophysiology simulator for in-silico experiments. URL: https://opencarp.org'
OpenCoarrays'OpenCoarrays is an open-source software project that supports the coarray Fortran (CAF) parallel programming features of the Fortran 2008 standard and several features proposed for Fortran 2015 in the draft Technical Specification TS 18508 Additional Parallel Features in Fortran. URL: https://github.com/sourceryinstitute/opencoarrays'
OpenColorIO' OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation.'
OpenCV'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. URL: https://opencv.org/'
opencv_contrib'OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.'
Open-Data-Cube-Core' 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. URL: https://github.com/opendatacube/datacube-core'
OpenEXR'OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications URL: https://www.openexr.com/'
OpenFAST' OpenFAST is an open-source wind turbine simulation tool that was established in 2017 with the FAST v8 code as its starting point (see FAST v8 and the transition to OpenFAST). OpenFAST is a multi-physics, multi-fidelity tool for simulating the coupled dynamic response of wind turbines.'
OpenFOAM'Description: OpenFOAM 2.4.0 plus the MicroNanoFlow Group Codes URL: https://github.com/MicroNanoFlows/OpenFOAM-2.4.0-MNF'
OpenFOAM-Extend'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. URL: http://www.extend-project.de/'
OpenForceField'Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications. URL: https://github.com/openforcefield/openforcefield/releases'
OpenGL' 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. '
OpenImageIO'OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. URL: https://openimageio.org/'
OpenJPEG'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. URL: https://www.openjpeg.org/'
OpenKIM-API'Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It 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 have to be installed by the user by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. URL: https://openkim.org/'
openkim-models'Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild installs the models. The API itself is in the kim-api package. URL: https://openkim.org/'
OpenMC' OpenMC is a Monte Carlo particle transport simulation code focused on neutron criticality calculations. It is capable of simulating 3D models based on constructive solid geometry with second-order surfaces. OpenMC supports either continuous-energy or multi-group transport. '
OpenMM'OpenMM is a toolkit for molecular simulation. URL: http://openmm.org'
OpenMMTools'A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages. URL: https://github.com/choderalab/openmmtools'
OpenMolcas'OpenMolcas is a quantum chemistry software package URL: https://gitlab.com/Molcas/OpenMolcas'
OpenMPI'The Open MPI Project is an open source MPI-3 implementation. URL: https://www.open-mpi.org/'
OpenMS'As part of the deNBI Center for integrative Bioinformatics, OpenMS offers an open-source software C-- library (- python bindings) for LC/MS data management and analyses. It provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it. URL: https://www.openms.de/'
OpenMX' OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. URL: http://www.openmx-square.org/'
OpenPGM' 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. URL: https://code.google.com/p/openpgm/'
OpenPhase' OpenPhase is the open source software project targeted at the phase field simulations of complex scientific problems involving microstructure formation in systems undergoing first order phase transformation.'
OpenPIV'OpenPIV is an open source Particle Image Velocimetry analysis software URL: http://www.openpiv.net'
openpyxl'A Python library to read/write Excel 2010 xlsx/xlsm files URL: https://openpyxl.readthedocs.io'
OpenSees'Open System for Earthquake Engineering Simulation URL: https://opensees.berkeley.edu/index.php'
OpenSlide'OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). URL: https://openslide.org/'
openslide-python'OpenSlide Python is a Python interface to the OpenSlide library. URL: https://github.com/openslide/openslide-python Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
OpenSSL'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. URL: https://www.openssl.org/'
OPERA'An optimal genome scaffolding program'
OPERA-MS'OPERA-MS is a hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies. URL: https://github.com/CSB5/OPERA-MS'
OptiType' OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. '
orca'Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line. URL: https://github.com/plotly/orca'
ORCA-HPRC-License'License terms for using ORCA on TAMU HPRC clusters'
ORFfinder' ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. URL: https://www.ncbi.nlm.nih.gov/orffinder'
OrfM'A simple and not slow open reading frame (ORF) caller.'
OrthoFinder'OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics URL: https://github.com/davidemms/OrthoFinder'
Osi'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. URL: https://github.com/coin-or/Osi'
OSPREY' OSPREY is a suite of programs for computational structure-based protein design.'
OSU-Micro-Benchmarks'OSU Micro-Benchmarks URL: https://mvapich.cse.ohio-state.edu/benchmarks/'
OTF' The Open Trace Format is a highly scalable, memory efficient event trace data format plus support library. It is the standard trace format for Vampir, and is open for other tools. [NOW OBSOLETE: use OTF2]'
OTF2' The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools. URL: https://www.score-p.org'
OVITO' OVITO is a scientific visualization and analysis software for atomistic simulation data URL: https://www.ovito.org/'
P3DFFT' Parallel Three-Dimensional Fast Fourier Transforms, dubbed P3DFFT, as well as its extension P3DFFT--, is a library for large-scale computer simulations on parallel platforms.This project was initiated at San Diego Supercomputer Center (SDSC) at UC San Diego by its main author Dmitry Pekurovsky, Ph.D.'
p4est'p4est is a C library to manage a collection (a forest) of multiple connected adaptive quadtrees or octrees in parallel. URL: http://www.p4est.org'
p4vasp'Visualization suite for VASP URL: http://www.p4vasp.at/'
p7zip'p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.'
packmol'Packing Optimization for Molecular Dynamics Simulations'
PAML'PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.'
pandas'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. URL: https://pypi.python.org/pypi/pandas/'
PANDAseq'PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.'
Pandoc'If you need to convert files from one markup format into another, pandoc is your swiss-army knife URL: https://pandoc.org'
Pango'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. URL: https://www.pango.org/'
Pangomm' The Pangomm package provides a C-- interface to Pango. '
PAPI' 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. URL: https://icl.cs.utk.edu/projects/papi/'
parallel'parallel: Build and execute shell commands in parallel URL: https://savannah.gnu.org/projects/parallel/'
parallel-fastq-dump'parallel fastq-dump wrapper URL: https://github.com/rvalieris/parallel-fastq-dump'
parasail'parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. URL: https://github.com/jeffdaily/parasail'
ParaView'ParaView is a scientific parallel visualizer. URL: https://www.paraview.org'
ParFlow' ParFlow is an integrated, parallel watershed model that makes use of high-performance computing to simulate surface and subsurface fluid flow. URL: http://computation.llnl.gov/casc/parflow/'
ParmEd'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. URL: https://parmed.github.io/ParmEd'
ParMETIS'ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.'
ParMGridGen'ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. URL: http://www-users.cs.umn.edu/~moulitsa/software.html'
PartitionFinder'PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks. URL: https://www.robertlanfear.com/partitionfinder'
PaStiX' PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods. URL: http://pastix.gforge.inria.fr/'
patchelf'PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. URL: https://github.com/NixOS/patchelf'
pauvre'Tools for plotting Oxford Nanopore and other long-read data URL: https://github.com/conchoecia/pauvre'
pbbam'The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. URL: http://pbbam.readthedocs.io/'
pbcopper'The pbcopper library provides a suite of data structures, algorithms, and utilities for C-- applications. URL: https://github.com/PacificBiosciences/pbcopper'
pbmm2'A minimap2 frontend for PacBio native data formats URL: https://github.com/PacificBiosciences/pbmm2'
PCAngsd'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.'
PCL'The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing.'
PCMSolver'An API for the Polarizable Continuum Model.'
PCRaster'PCRaster Is a collection of software targeted at the development and deployment of spatio-temporal environmental models.'
PCRE' The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. URL: https://www.pcre.org/'
PCRE2' The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. URL: https://www.pcre.org/'
PDT' Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. URL: https://www.cs.uoregon.edu/research/pdt/'
PennCNV'A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. URL: https://penncnv.openbioinformatics.org/'
Perl'Larry Wall's Practical Extraction and Report Language URL: https://www.perl.org/'
PerlCyc'Perlcyc.pm is a Perl module for accessing internal Pathway-Tools functions. URL: https://pmn.dpb.carnegiescience.edu/'
perli' perli is a multi-platform Perl REPL (read-eval-print-loop) for interactive experimentation with Perl code, convenient documentation lookups, and quick computations. URL: https://github.com/mklement0/perli'
PERL_TAMU(description not available)
PEST++'PEST-- is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model. URL: https://github.com/usgs/pestpp'
PETSc'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. URL: https://www.mcs.anl.gov/petsc'
petsc4py'petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.'
pFUnit'pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran. URL: http://pfunit.sourceforge.net'
PGI'C, C-- and Fortran compilers from The Portland Group - PGI URL: https://www.pgroup.com/'
PHAST'PHAST is a freely available software package for comparative and evolutionary genomics.'
PheWAS'Provides an accessible R interface to the phenome wide association study. URL: https://www.vumc.org/cpm/center-precision-medicine-blog/phewas-r-package'
PhiPack'The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well. URL: http://www.maths.otago.ac.nz/~dbryant/software.html'
Phobius'Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. URL: http://phobius.sbc.su.se'
phonemizer' The phonemizer allows simple phonemization of words and texts in many languages. Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. It is using four backends: espeak, espeak-mbrola, festival and segments. URL: https://github.com/bootphon/phonemizer'
phono3py'phono3py calculates phonon-phonon interaction and related properties using the supercell approach.'
phonopy'Phonopy is an open source package of phonon calculations based on the supercell approach. URL: https://atztogo.github.io/phonopy/'
PHYLIP'PHYLIP is a free package of programs for inferring phylogenies.'
phylokit'C-- library for high performance phylogenetics URL: https://github.com/pranjalv123/phylokit'
phylonaut'Dynamic programming for phylogenetics applications URL: https://github.com/pranjalv123/phylonaut'
PhyloNet'PhyloNet is a tool designed mainly for analyzing, reconstructing, and evaluating reticulate (or non-treelike) evolutionary relationships, generally known as phylogenetic networks. URL: https://bioinfocs.rice.edu/phylonet'
PhyloNetworks'PhyloNetworks is a Julia package for the manipulation, visualization, inference of phylogenetic networks, and their use for trait evolution.'
PhyloSNP'PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data. URL: https://hive.biochemistry.gwu.edu/phylosnp'
PhyML'Phylogenetic estimation using (Maximum) Likelihood URL: https://github.com/stephaneguindon/phyml'
phyx'phyx performs phylogenetics analyses on trees and sequences. URL: https://github.com/FePhyFoFum/phyx'
picard'A set of tools (in Java) for working with next generation sequencing data in the BAM format. URL: https://sourceforge.net/projects/picard'
PICRUSt' PICRUSt (pronounced 'pie crust') is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. URL: http://picrust.github.io/picrust/index.html'
pigz' 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. URL: https://zlib.net/pigz/'
PIL'The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. URL: http://www.pythonware.com/products/pil'
Pillow'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. URL: https://pillow.readthedocs.org/'
Pillow-SIMD'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. URL: https://github.com/uploadcare/pillow-simd Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default)'
Pilon' Pilon is an automated genome assembly improvement and variant detection tool URL: https://github.com/broadinstitute/pilon'
pip'The PyPA recommended tool for installing Python packages.'
piPipes'piPipes is a set of pipelines developed in the Zamore Lab and ZLab to analyze piRNA/transposon from different Next Generation Sequencing libraries (small RNA-seq, RNA-seq, Genome-seq, ChIP-seq, CAGE/Degradome-Seq)..'
pIRS'pIRS (profile based Illumina pair-end Reads Simulator) is a program for simulating paired-end reads from a reference genome. It is optimized for simulating reads similar to those generated from the Illumina platform. URL: https://github.com/galaxy001/pirs'
pixman' 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. URL: http://www.pixman.org/'
pizzly'Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.'
pkgconfig'pkgconfig is a Python module to interface with the pkg-config command line tool URL: https://github.com/matze/pkgconfig'
pkg-config' 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). URL: https://www.freedesktop.org/wiki/Software/pkg-config/'
PlantClusterFinder'A pipeline to predict metabolic gene clusters from plant genomes URL: https://pmn.dpb.carnegiescience.edu/'
plantcv'PlantCV: Plant phenotyping using computer vision. URL: https://pypi.org/project/plantcv/'
PlaScope'Plasmid exploration of bacterial genomes URL: https://github.com/GuilhemRoyer/PlaScope'
PlasmaPy'Open source Python ecosystem for plasma research and education URL: https://www.plasmapy.org'
Platanus'PLATform for Assembling NUcleotide Sequences'
plc' plc is the public Planck Likelihood Code. It provides C and Fortran libraries that allow users to compute the log likelihoods of the temperature, polarization, and lensing maps. Optionally, it also provides a python version of this library, as well as tools to modify the predetermined options for some likelihoods (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature). URL: http://pla.esac.esa.int/pla/#home'
PLINK' 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. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). URL: https://www.cog-genomics.org/plink/1.9'
PLINKSEQ' PLINK/SEQ is an open-source C/C-- library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package. '
Ploticus'Ploticus is a free GPL software utility that can produce various types of plots and graphs'
plotly'Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. URL: https://cran.r-project.org/web/packages/plotly'
plotly.py'An open-source, interactive graphing library for Python URL: https://plot.ly/python Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
PLUMED'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. URL: https://www.plumed.org'
PLY'PLY is yet another implementation of lex and yacc for Python.'
plyrhttps://github.com/hadley/plyr 'Tools for Splitting, Applying and Combining Data'
PMIx'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. URL: https://pmix.org/'
PnetCDF'Parallel netCDF: A Parallel I/O Library for NetCDF File Access URL: https://trac.mcs.anl.gov/projects/parallel-netcdf'
pocl'Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard URL: https://portablecl.org'
poetry'Python packaging and dependency management made easy URL: https://python-poetry.org/'
polymake'polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects. URL: https://polymake.org'
pompi'Toolchain with PGI C, C-- and Fortran compilers, alongside OpenMPI. URL: http://www.pgroup.com/index.htm'
poppler'Poppler is a PDF rendering library based on the xpdf-3.0 code base. URL: https://poppler.freedesktop.org/'
popscle'A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools URL: https://github.com/statgen/popscle'
popSTR'PopSTR - A Population based microsatellite genotyper URL: https://github.com/DecodeGenetics/popSTR'
Porechop'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 URL: https://github.com/rrwick/Porechop'
poretools'A toolkit for working with nanopore sequencing data from Oxford Nanopore.'
PostgreSQL'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. URL: https://www.postgresql.org/'
POT'POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems related to Optimal Transport for signal, image processing and machine learning.'
POV-Ray'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 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. URL: http://matsen.fhcrc.org/pplacer/'
PRANK' 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.'
PRAP'PRAP is a platform independent Python3 tool used to analyze pan-resistome characteristics for multiple genomes. URL: https://github.com/syyrjx-hyc/PRAP'
preCICE'preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations, including, but not restricted to fluid-structure interaction and conjugate heat transfer simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. This allows for the high flexibility that is needed to keep a decent time-to-solution for complex multi-physics scenarios. URL: https://www.precice.org/'
preseq'Software for predicting library complexity and genome coverage in high-throughput sequencing.'
pretty-yaml'PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc). URL: https://github.com/mk-fg/pretty-yaml Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
Primer3'Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.'
PRINSEQ'A bioinformatics tool to PRe-process and show INformation of SEQuence data. URL: http://prinseq.sourceforge.net'
printproto'X.org PrintProto protocol headers.'
PRISMS-PF'PRISMS-PF is a powerful, massively parallel finite element code for conducting phase field and other related simulations of microstructural evolution. URL: https://prisms-center.github.io/phaseField'
prodigal'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. URL: https://github.com/hyattpd/Prodigal/'
progressbar33'Text progress bar library for Python.'
PROJ'Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates URL: https://proj.org'
ProjectQ'An open source software framework for quantum computing'
prokka'Prokka is a software tool for the rapid annotation of prokaryotic genomes. URL: https://www.vicbioinformatics.com/software.prokka.shtml'
Proteinortho'Proteinortho is a tool to detect orthologous genes within different species.'