Software Modules on the Ada Cluster

Last Updated: May 7 12:50:02 CDT

The available software for the Ada 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
3to2' lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.'
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.'
ABACAS2'ABACAS2, a tool for ordering and orientating biosequences along a reference'
ABAQUS'Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. URL:'
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.'
ABRA2'ABRA2 is an updated implementation of ABRA featuring: RNA support, Improved scalability (Human whole genomes now supported), Improved accuracy, Improved stability and usability (BWA is no longer required to run ABRA although we do recommend BWA as the initial aligner for DNA) URL:'
ABRicate'Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: Resfinder, CARD, ARG-ANNOT, NCBI BARRGD, NCBI, EcOH, PlasmidFinder, Ecoli_VF and VFDB. URL:'
absl-py'Abseil Python Common Libraries'
ABySS'Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler URL:'
ACML'ACML provides a free set of thoroughly optimized and threaded math routines for HPC, scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. '
ACT' ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. URL:'
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:'
adjustText'A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.'
ADMIXTURE' ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. URL:'
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:'
AFNI'AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.'
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:'
AGFusion'AGFusion is a python package for annotating gene fusions from the human or mouse genomes. URL:'
aiohttp'" Async http client/server framework '
Albacore' Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms.'
Algorithm-Loops' Algorithm::Loops - Looping constructs: NestedLoops, MapCar-, Filter, and NextPermute- URL:'
almaBTE' The almaBTE software package developed by this project extends the ShengBTE approach currently employed for homogeneous bulk materials, into the mesoscale, to fully describe thermal transport from the electronic ab initio level, through the atomistic one, all the way into the mesoscopic structure level.'
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:'
Amara'Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML. URL:'
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.'
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:'
AMPL-MP' An open-source library for mathematical programming. URL:'
AMRFinderPlus'NCBI Antimicrobial Resistance Gene Finder Plus URL:'
Anaconda'Anaconda environment for'
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:'
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:'
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:'
ANNOVAR' ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).'
ANSYS' ANSYS 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:'
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:'
antiSMASH'antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. URL:'
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:'
anvio'An analysis and visualization platform for 'omics data. URL:'
any2fasta'Convert various sequence formats to FASTA URL:'
APR'Apache Portable Runtime (APR) libraries. URL:'
APR-util'Apache Portable Runtime (APR) util libraries. URL:'
Aragorn' tRNA (and tmRNA) detection'
archspec'A library for detecting, labeling, and reasoning about microarchitectures URL:'
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:'
ARKS' Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. This project is a new kmer-based (alignment free) implementation of ARCS. URL:'
Arlequin'Arlequin: An Integrated Software for Population Genetics Data Analysis URL:'
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:'
arpack-ng'ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. URL:'
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:'
Arrow'Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform for in-memory data. URL:'
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:'
ArviZ'Exploratory analysis of Bayesian models with Python URL:'
ASAP3'ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). URL:'
ASE'ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed. URL:'
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:'
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:'
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:'
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:'
Atkmm' Atkmm is the official C-- interface for the ATK accessibility toolkit library. '
ATLAS'ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library.'
ATOMEYE(description not available)
atools'Tools to make using job arrays a lot more convenient. URL:'
at-spi2-atk'AT-SPI 2 toolkit bridge URL:'
at-spi2-core' Assistive Technology Service Provider Interface. URL:'
attr'Commands for Manipulating Filesystem Extended Attributes URL:'
augur'Pipeline components for real-time phylodynamic analysis URL:'
AUGUSTUS'AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences URL:'
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.'
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:'
AutoDock_Vina' AutoDock Vina is an open-source program for doing molecular docking. '
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:'
Automake'Automake: GNU Standards-compliant Makefile generator URL:'
AutoMap'Tool to find regions of homozygosity (ROHs) from sequencing data. URL:'
Autotools' This bundle collect the standard GNU build tools: Autoconf, Automake and libtool URL:'
b2b-utils'This package contains a set of programs and utilities for working with genomic data. URL:'
BactSNP'BactSNP is a tool to identify SNPs among bacterial isolates.'
Bader'A fast algorithm for doing Bader's analysis on a charge density grid.'
BaitFisher-package'BaitFisher was been designed to construct hybrid enrichment baits from multiple sequence alignments (MSAs) or annotated features in MSAs. URL:'
bamkit'Tools for common BAM file manipulations URL:'
BAMM'BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a program for modeling complex dynamics of speciation, extinction, and trait evolution on phylogenetic trees. URL:'
bam-read' A tool for reading BAM files developed exclusively by the Transrate tool.'
bam-readcount'Count DNA sequence reads in BAM files URL:'
BamTools'BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.'
Barnap' Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).'
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'
bat'The BAT Python package supports the processing and analysis of Bro data with Pandas, scikit-learn, and Spark'
Bazel'Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. URL:'
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:'
BBMap'BBMap short read aligner, and other bioinformatic tools. URL:'
bcbio-nextgen' A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. '
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:'
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:'
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:'
BEAGLE'Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.'
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:'
BeautifulSoup'Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. URL:'
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:'
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:'
BESST' BESST is a package for scaffolding genomic assemblies. It contains several modules for e.g. building a "contig graph" from available information, obtaining scaffolds from this graph, and accurate gap size information. '
BGLR' Bayesian Generalized Linear Regression. '
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:'
BinSanity'BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes. URL:'
binutils'binutils: GNU binary utilities URL:'
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. '
Bio-DB-HTS'Read files using HTSlib including BAM/CRAM, Tabix and BCF database files URL:'
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:'
Bio-EUtilities'BioPerl low-level API for retrieving and storing data from NCBI eUtils URL:'
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:'
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.'
Bio-MLST-Check'High throughput multilocus sequence typing (MLST) checking. URL:'
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:'
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:'
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:'
BioRuby'BioRuby is an open source Ruby library for developing bioinformatics software. URL:'
Bismark'A tool to map bisulfite converted sequence reads and determine cytosine methylation states URL:'
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:'
bitarray'bitarray provides an object type which efficiently represents an array of booleans'
BitSeq' BitSeq (Bayesian Inference of Transcripts from Sequencing Data) is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts. URL:'
blasr' This is an unsupported fork of the PacBio blasr aligner. It contains my (very beta) optimizations and new functionality. It may disappear at any time. URL:'
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:'
BLAT'BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.'
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:'
BLIS'BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. URL:'
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 URL:'
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:'
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.'
bmon' bmon is a monitoring and debugging tool to capture networking related statistics and prepare them visually in a human friendly way.'
bmtagger'Best Match Tagger for removing human reads from metagenomics datasets URL:'
bokeh'Statistical and novel interactive HTML plots for Python URL:'
BoltzTraP2'band-structure interpolator and transport coefficient calculator'
Boost'Boost provides free peer-reviewed portable C-- source libraries. URL:'
Boost.Python'Boost.Python is a C-- library which enables seamless interoperability between C-- and the Python programming language. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-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:'
Bowtie'Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. URL:'
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:'
BPP' BPP is a Bayesian Markov chain Monte Carlo (MCMC) program for analyzing DNA sequence alignments from multiple loci and multiple closely-related species under the multispecies coalescent (MSC) model URL:'
BreakDancer'BreakDancer is a Perl/C-- package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads URL:'
breseq'breseq is a computational pipeline for the analysis of short-read re-sequencing data URL:'
BroadPeak' BroadPeak broad peak calling algorithm for diffuse ChIP-seq datasets. '
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: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
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.'
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:'
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:'
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: 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:'
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:'
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:'
cachetools' This module provides various memoizing collections and decorators, including variants of the Python Standard Library’s @lru_cache function decorator. URL:'
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:'
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:'
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.'
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:'
cairocffi'cffi-based cairo bindings for Python'
cairomm' The Cairomm package provides a C-- interface to Cairo. '
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:'
Canu' Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). URL:'
CapnProto'Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.'
Cargo'The Rust package manager'
Cartopy'Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy. URL:'
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.'
causalml' Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML URL:'
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:'
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:'
cclib'parsers and algorithms for computational chemistry URL:'
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:'
CDO'CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. URL:'
cdsapi'Climate Data Store API URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
CEGMA'CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. '
CellRanger'Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. URL:'
Centrifuge'Classifier for metagenomic sequences URL:'
CESM'The Community Earth System Model (CESM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CESM allows researchers to conduct fundamental research into the earth's past, present and future climate states.'
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:'
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:'
cftime'Time-handling functionality from netcdf4-python'
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:'
CGAT' CGAT is a collection of tools for the computational genomicist written in the python language. '
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:'
CGmapTools'Command-line Toolset for Bisulfite Sequencing Data Analysis URL:'
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.'
Charm++'Charm-- is a parallel programming framework in C--, supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers.'
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:'
CheckM'CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. URL:'
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. URL:'
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. '
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:'
ciftify'The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets'
Circlator'Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.'
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:'
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:'
Clang'C, C--, Objective-C compiler, based on LLVM. Does not include C-- standard library -- use libstdc-- from GCC. URL:'
Clang-Python-bindings'Python bindings for libclang URL:'
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:'
click'A simple wrapper around optparse for powerful command line utilities.'
CLIPper'CLIPper is a tool to define peaks in your CLIP-seq dataset. URL:'
CLISP' Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. URL:'
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:'
ClustAGE'ClustAGE is a command-line tool built using the Perl scripting language for the purpose of analyzing and comparing accessory genomic elements (AGEs) between genomes. URL:'
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.'
CMake' CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. URL:'
CNVkit'A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. URL:'
CNVnator'A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads. URL:'
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:'
colorama'Cross-platform colored terminal text.'
colorspace'Color Space Manipulation'
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.'
configparser'configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5'
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.'
CONTRA' CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. CONTRA calls copy number gains and losses for each target region with key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. It takes standard alignment formats (BAM/SAM) and output in variant call format (VCF 4.0) for easy integration with other next generation sequencing analysis package.'
ConvergeCFD'Converge CFD software by Convergent Science URL:'
ConvergeStudio'Converge Studio software by Convergent Science '
CoordgenLibs'Schrodinger-developed 2D Coordinate Generation URL:'
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:'
corner'Make some beautiful corner plots. URL:'
coverage' is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not.'
CoverM'CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. URL:'
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:'
CPLEX'IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability.'
CppUnit' CppUnit is the C-- port of the famous JUnit framework for unit testing. URL:'
cram'Cram is a functional testing framework for command line applications. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
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:'
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:'
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:'
cryptography'cryptography is a package which provides cryptographic recipes and primitives to Python developers..'
csvkit'csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. URL:'
CTK'The CLIP Tool Kit (CTK) is a software package that provides a set of tools for analysis of CLIP data starting from the raw reads generated by the sequencer. URL:'
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:'
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:'
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:'
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.'
cuDNN'The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. URL:'
Cufflinks'Transcript assembly, differential expression, and differential regulation for RNA-Seq'
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:'
cutadapt'Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. URL:'
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:'
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:'
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:'
CyToolz'Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries.'
cytosim'Cytosim is a cytoskeleton simulation engine written in C-- working on Mac OS, GNU/Linux and Windows (with Cygwin). URL:'
cyvcf2'cython - htslib == fast VCF and BCF processing URL: 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:'
damageproto' Monitoring the regions affected by rendering has wide-spread use, from VNC-like systems scraping the screen to screen magnifying applications designed to aid users with limited visual acuity. The DAMAGE extension is designed to make such applications reasonably efficient in the face of server-client latency. '
Dashing'Dashing sketches and computes distances between fasta and fastq data.'
dask'Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. URL:'
datamash'GNU datamash performs basic numeric, textual and statistical operations on input data files URL:'
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:'
DAZZ_DB'The Dazzler Database library URL:'
DB'Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. URL:'
DBD-mysql'Perl binding for MySQL'
DB_File'Perl5 access to Berkeley DB version 1.x.'
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:'
dbus-glib'D-Bus is a message bus system, a simple way for applications to talk to one another. URL:'
dDocent'dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing. If you have a reference already, dDocent can be used to call SNPs from almost any type of NGS data set. URL:'
dealii' deal.II is a C-- software library supporting the creation of finite element codes and an open community of users and developers. '
deal.II'deal.II is a C-- program library targeted at the computational solution of partial differential equations using adaptive finite elements. URL:'
deepdiff'DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. URL:'
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:'
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:'
Delly'Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. URL:'
DendroPy'A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
DEXTRACTOR'The Dextractor commands allow one to pull exactly and only the information needed for assembly and reconstruction from the source HDF5 files produced by the PacBio RS II sequencer, or from the source BAM files produced by the PacBio Sequel sequencer.'
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:'
DFT-D3'DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. URL:'
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:'
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:'
DIAMOND'DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. URL:'
dichromat'Color Schemes for Dichromats'
DIDA'DIDA is a novel framework that performs the large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes. '
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: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
discovar'DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants. '
dispy' Distributed and Parallel Computing with/for Python.'
dlib'Description:Dlib is a modern C-- toolkit containing machine learning algorithms and tools for creating complex software in C-- to solve real world problems. URL:'
DL_POLY_Classic'DL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package. URL:'
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:'
Docutils' Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.'
DOLFIN'DOLFIN is the C--/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.'
DomainFinder' Converts manually curated CATH structural domain hierarchy used to search UniProt, RefSeq and Ensembl protein sequences into simple multi-domain architectures'
dos2unix'UNIX to DOS/MAC and vice versa text file format converter'
dotNET-SDK'.NET is a free, cross-platform, open source developer platform for building many different types of applications. URL:'
double-conversion'Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. URL:'
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:'
DRACO'DRACO: Deconvolution of RNA Alternative COnformations URL:'
Dsuite'Fast calculation of the ABBA-BABA statistics across many populations/species URL:'
dtcmp' Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI URL:'
dtcwt'Dual-Tree Complex Wavelet Transform library for Python URL:'
E2P2'Ensemble-based Enzyme Prediction Program (E2P2) predicts metabolic enzymes in a sequenced genome. URL:'
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:'
EasyBuild-ada'EasyBuild environment variables for building system software on'
EasyBuild-ada-myeb'User EasyBuild environment for in $SCRATCH/eb'
EasyBuild-ada-R'EasyBuild environment variables for building software for the experimental R_modules on'
EasyBuild-ada-restricted-amber'EasyBuild environment variables for building restricted software Amber on'
EasyBuild-ada-restricted-charmmlite'EasyBuild environment variables for building restricted software on'
EasyBuild-ada-restricted-econstat'EasyBuild environment variables for building restricted software for the econstat group on'
EasyBuild-ada-restricted-fdtd'EasyBuild environment variables for building restricted software on'
EasyBuild-ada-restricted-junjiez'EasyBuild environment variables for building software on for the junjiez group'
EasyBuild-ada-restricted-math_madymo'EasyBuild environment variables for building restricted software Amber on'
EasyBuild-ada-restricted-orca'EasyBuild environment variables for building restricted software for ORCA on'
EasyBuild-ada-restricted-taborgrp'EasyBuild environment variables for building restricted software on'
EasyBuild-ada-restricted-tamamis-shared'EasyBuild environment variables for building restricted software for group tamamis-shared'
EasyBuild-ada-restricted-tamusc'EasyBuild environment variables for building restricted software for HPRC on'
EasyBuild-ada-restricted-tecplotgrp'EasyBuild environment variables for building restricted software Amber on'
EasyBuild-ada-restricted-vasp'EasyBuild environment variables for building restricted software VASP on'
EasyBuild-ada-SCRATCH'User EasyBuild environment for in $SCRATCH/eb'
ea-utils'Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.'
eb-python' Python is a programming language that lets you work more quickly and integrate your systems more effectively. This package is soley for the use of EasyBuild on RHEL6/Centos6 which only has python-2.6.6. URL:'
eb-tutorial'EasyBuild tutorial example URL:'
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:'
ecoPCR'ecoPCR helps you estimate Barcode primers quality. In conjunction with OBITools, you can postprocess ecoPCR output to compute barcode coverage and barcode specificity. URL:'
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:'
edlib'Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. URL:'
EffHunter'EffHunter produces ab initio predictions of canonical effectors proteins using a total proteome. URL:'
Eigen'Eigen is a C-- template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. URL:'
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:'
elfutils' The elfutils project provides libraries and tools for ELF files and DWARF data. URL:'
ELI5' ELI5 is a Python package which helps to debug machine learning classifiers and explain their predictions.'
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:'
ELPA'Eigenvalue SoLvers for Petaflop-Applications . URL:'
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:'
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:'
EMAN2' EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. URL:'
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: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
EMU'EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets URL:'
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:'
ensembl'Ensembl Core API'
ensembl-compara'The ensembl-io repo is intended as a shared codebase for handling the parsing and writing of popular biological formats used by Ensembl, such as BED, BigWig and FASTA. For a full list of supported formats, see the child objects in modules/Bio/EnsEMBL/IO/Parser/.'
ensembl-funcgen'The Funcgen database contains currently 4 different types of data which can be accessed through the API. 1. Regulatory Features 2. Segmentation 3. Microarray Probe Mappings 4. External Regulatory Data'
ensembl-io'The ensembl-io repo is intended as a shared codebase for handling the parsing and writing of popular biological formats used by Ensembl, such as BED, BigWig and FASTA. For a full list of supported formats, see the child objects in modules/Bio/EnsEMBL/IO/Parser/.'
ensembl-variation'The Ensembl Variation API (Application Programme Interface) serves as a middle layer between the underlying MySQL database and the user's script. It aims to encapsulate the database layout by providing high level access to the database.'
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. '
entrypoints'Entry points are a way for Python packages to advertise objects with some common interface.'
ESMF'The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. URL:'
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:'
Essentia'Open-source library and tools for audio and music analysis, description and synthesis URL:'
eta' ETA Progress bar for command-line utilities'
ETE'A Python framework for the analysis and visualization of trees URL:'
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.'
EVidenceModeler'The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. URL:'
EvidentialGene'EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.'
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:'
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:'
export2graphlan'export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.'
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:'
faac'A complete, cross-platform solution to record, convert and stream audio and video.'
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: 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 URL:'
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:'
fastahack' tahack is a small application for indexing and extracting sequences and subsequences from FASTA files. The included Fasta.cpp library provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.'
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:'
FastME'FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. URL:'
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:'
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:'
fastq-join' fastq-join joins two paired-end reads on the overlapping ends.'
FastQScreen' 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. URL:'
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:'
fastsimcoal2'fast sequential Markov coalescent simulation of genomic data under complex evolutionary models URL:'
fastStructure' A variational framework for inferring population structure from SNP genotype data.'
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:'
FastViromeExplorer'Identify the viruses/phages and their abundance in the viral metagenomics data. URL:'
FASTX-Toolkit'The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. URL:'
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:'
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:'
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:'
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'
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:'
File-Copy-Link'The distribution File-Copy-Link includes the modules File::Spec::Link and File::Copy::Link and the script copylink. They include routines to read and copy links.'
Filtlong' Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.'
FimTyper'FimTyper identifies the FimH type in total or partial sequenced isolates of E. coli. URL:'
fineRADstructure'A package for population structure inference from RAD-seq data URL:'
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:'
fixesproto' FixesProto protocol headers.'
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:'
flatbuffers'FlatBuffers: Memory Efficient Serialization Library URL:'
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:'
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:'
Flye'Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. URL:'
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'
fmt'fmt (formerly cppformat) is an open-source formatting library. URL:'
fontconfig' Fontconfig is a library designed to provide system-wide font configuration, customization and application access. URL:'
foss'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. URL:'
fosscuda'GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
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.'
FreeBayes' FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. '
freeglut'freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. URL:'
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:'
FreeSASA'FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA). URL:'
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:'
FreeXL' FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. URL:'
FriBidi' The Free Implementation of the Unicode Bidirectional Algorithm. URL:'
FSL'FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. URL:'
fsspec'A specification for pythonic filesystems. URL:'
FTGL' FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL ( applications. URL:'
FuSeq'FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data. URL:'
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:'
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:'
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:'
GAMESS_tamu'"Description:TAMU HPRC GAMESS launcher - rungms " "'
GAM-NGS' Genomic assemblies merger for next generation sequencing'
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.'
GapFiller' GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds. It is unique in offering the possibility to manually control the gap closure process. By using the distance information of paired-read data, GapFiller seeks to close the gap from each edge in an iterative manner. From a good number of tests we see the program yields excellent results both on bacterial en eukaryotic data sets. The command-line Perl script and additional files can be downloaded below. The input data is given by pre-assembled scaffold sequences (FASTA) and NGS paired-read data (FASTA or FASTQ). The final gap-filled scaffolds are provided in FASTA format. '
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:'
gatb-core' You can use the GATB-Core library to develop new NGS data analysis softwares. URL:'
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: 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:'
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:'
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:'
gcccuda'GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.'
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. URL:'
GD' - Interface to Gd Graphics Library URL:'
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:'
GDB'The GNU Project Debugger'
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 provides a standard client-based mechanism in support of high-performance data downloads and submission.'
GDCHART'Easy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format. URL:'
GDCM'Grassroots DICOM: Cross-platform DICOM implementation URL:'
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:'
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:'
gearshifft'Benchmark Suite for Heterogenuous FFT Implementations'
GEM'GEM is a scientific software for studying protein-DNA interaction at high resolution using ChIP-seq/ChIP-exo data. It can also be applied to CLIP-seq and Branch-seq data. URL:'
Gemini' GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. '
GEMMA'Genome-wide Efficient Mixed Model Association URL:'
geneid'geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. '
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.'
GeneMarkS'GeneMarkS - Gene Prediction in Prokaryotes.'
gengetopt'Gengetopt is a tool to write command line option parsing code for C programs. URL:'
GenomeMapper' GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference.'
GenomeTools'A comprehensive software library for efficient processing of structured genome annotations. URL:'
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:'
GEOS'GEOS (Geometry Engine - Open Source) is a C-- port of the Java Topology Suite (JTS) URL:'
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:'
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:'
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:'
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:'
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:'
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:'
gimpi'GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI.'
giolf'GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
GIREMI'GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data. URL:'
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:'
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 URL:'
GitPython' GitPython is a python library used to interact with Git repositories URL:'
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:'
Glade' Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK- toolkit and the GNOME desktop environment.'
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:'
GLib'GLib is one of the base libraries of the GTK- project URL:'
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:'
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:'
GlobalArrays'Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model URL:'
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: 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:'
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:'
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:'
GMP' GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. URL:'
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: 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:'
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:'
GNU'Compiler-only toolchain with GCC and binutils.'
gnuplot'Portable interactive, function plotting utility URL:'
gnutls'GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.'
Go'Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. URL:'
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:'
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.'
googletest'Google's C-- test framework URL:'
goolf'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
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:'
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:'
gperftools' gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. URL:'
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'
grabix' grabix leverages the fantastic BGZF library in samtools to provide random access into text files that have been compressed with bgzip. grabix creates it's own index (.gbi) of the bgzipped file. Once indexed, one can extract arbitrary lines from the file with the grab command. Or choose random lines with the, well, random command. '
Grace'Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. URL:'
gradunwarp'Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original. URL:'
GraphicsMagick'GraphicsMagick is the swiss army knife of image processing. URL:'
GraPhlAn'GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.'
GraphMap2'A highly sensitive and accurate mapper for long, error-prone reads URL:'
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:'
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:'
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:'
GRASS' GRASS GIS, commonly referred to as GRASS (Geographic Resources Analysis Support System), is a free and open source Geographic Information System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.'
gretl'A cross-platform software package for econometric analysis URL:'
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' GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds for both single and double precision. It also contains the gmxapi extension for the single precision MPI build. URL:'
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:'
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:'
gsport'GSPORT command-line tool for accessing GenomeScan Customer Portal URL:'
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.'
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:'
gtable'Arrange 'Grobs' in Tables'
GTDB-Tk'A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. URL:'
gtest'Google's framework for writing C-- tests on a variety of platforms URL:'
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:'
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:'
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:'
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:'
gzip'gzip (GNU zip) is a popular data compression program as a replacement for compress URL:'
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:'
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:'
Hadoop'Hadoop MapReduce by Cloudera URL:'
HAL'HAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. URL:'
HarfBuzz'HarfBuzz is an OpenType text shaping engine. URL:'
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:'
HarvestTools'HarvestTools is a part of the Harvest software suite and provides file conversion between Gingr files and various standard text formats'
HDDM'HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC). URL:'
HDF' HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. URL:'
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:'
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: 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:'
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:'
HeFFTe'Highly Efficient FFT for Exascale (HeFFTe) library URL:'
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:'
help2man'help2man produces simple manual pages from the '--help' and '--version' output of other commands. URL:'
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:'
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:'
HiCExplorer'HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization. URL:'
hisat'HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index. '
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:'
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:'
HMMER2'HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. URL:'
Homer'HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.'
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.'
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:'
htop'An interactive process viewer for Unix'
HTSeq'A framework to process and analyze data from high-throughput sequencing (HTS) assays URL:'
HTSlib'A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix URL:'
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. URL:'
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:'
HYCOM'HYCOM - HYbrid Coordinate Ocean Model'
hyperopt'Distributed Asynchronous Hyperparameter Optimization in Python URL:'
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:'
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:'
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:'
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:'
iccifort'Intel C, C-- & Fortran compilers URL:'
iccifortcuda'Intel C, C-- & Fortran compilers with CUDA toolkit'
IceT' The Image Composition Engine for Tiles (IceT) is a high-performance sort-last parallel rendering library.'
ICORN2'ICORN2 is a software to correct reference genome sequences. The main idea is to iteratively map reads and find differences in the sequence. '
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.'
ictce'Intel Cluster Toolkit Compiler Edition provides Intel C/C-- and Fortran compilers, Intel MPI & Intel MKL.'
ICU'ICU is a mature, widely used set of C/C-- and Java libraries providing Unicode and Globalization support for software applications. URL:'
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.'
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:'
IgBLAST'IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. URL:'
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:'
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:'
igv-reports'Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol. URL:'
IGVTools' This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also '
iimpi'Intel C/C-- and Fortran compilers, alongside Intel MPI. URL:'
iimpic'Intel C/C-- and Fortran compilers, alongside Intel MPI and CUDA.'
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:'
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: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
ImageMagick'ImageMagick is a software suite to create, edit, compose, or convert bitmap images URL:'
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:'
imbalanced-learn'imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.'
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:'
impi'Intel MPI Library, compatible with MPICH ABI URL:'
IMSindel'An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis. URL:'
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:'
inputproto' InputProto protocol headers.'
IntaRNA'Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites'
intel'Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). URL:'
intelcuda'Intel Cluster Toolkit Compiler Edition provides Intel C/C-- and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit'
INTEL-PARA(description not available)
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:'
intltool'intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. URL:'
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:'
iomkl'Intel Cluster Toolchain Compiler Edition provides Intel C/C-- and Fortran compilers, Intel MKL & OpenMPI. URL:'
iompi'Intel C/C-- and Fortran compilers, alongside Open MPI. URL:'
IOR' The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. URL:'
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:'
Ipopt'Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization. URL:'
IPSMPI(description not available)
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:'
IQ-TREE'Efficient phylogenomic software by maximum likelihood URL:'
iRAP'a flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression and testing for differential expression.'
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.'
ITK'Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. URL:'
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:'
itsdangerous' Various helpers to pass trusted data to untrusted environments and back.'
Jabba' Jabba, a hybrid error correction tool for sequencing reads.'
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:'
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:'
Java'Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. URL:'
JavaCyc'Javacyc is a java class for accessing internal Pathway-Tools functions. URL:'
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:'
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. URL:'
JCVI'Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. URL:'
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:'
jemalloc'jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. URL:'
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:'
joypy'Joyplots in Python with matplotlib & pandas URL:'
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:'
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:'
Judy'A C library that implements a dynamic array. URL:'
Juicer'Juicer is a one-click pipeline for processing terabase scale Hi-C datasets. URL:'
Juicer_tools'Tools for use with the Juicer application. URL:'
Julia'Julia is a high-level, high-performance dynamic programming language for numerical computing URL:'
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.'
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:'
Kaiju'Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments URL:'
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:'
Karect' KAUST Assembly Read Error Correction Tool'
KAT'The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra. URL:'
kbproto' KBProto protocol headers.'
kedro' Kedro is an open-source Python framework that applies software engineering best-practice to data and machine-learning pipelines. URL:'
Kent_tools'Kent utilities: collection of tools used by the UCSC genome browser. URL:'
Keras'Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.'
khmer' In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more URL:'
KILAPE' KILAPE (K-masking and Iterative Local Assembly of Paired Ends) is an automated scaffolding and gap filling software pipeline which predicts repetitive elements in Next Generation Sequencing read libraries without resorting to a reference sequence. To see executable files: ls $KILAPE_HOME; ls $KILAPE_BIN '
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:'
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:'
KMC'KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.'
KmerGenie'KmerGenie estimates the best k-mer length for genome de novo assembly. URL:'
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.'
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:'
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:'
KronaTools'Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.'
kSNP' kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP can take 100's of microbial genomes as input.'
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:'
KyotoCabinet'Kyoto Cabinet is a library of routines for managing a database. URL:'
labeling'Axis Labeling'
LAME'LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. URL:'
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:'
lapels' Lapels - A remapper and annotator of in silico (pseudo) genome alignments'
LAST'LAST finds similar regions between sequences. URL:'
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:'
LATTE' Open source density functional tight binding molecular dynamics.'
lavaan'lavaan is a free, open source R package for latent variable analysis URL:'
LCov'LCOV - the LTP GCOV extension'
LEfSe' LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.'
leidenalg'Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python. URL:'
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:'
libarchive' Multi-format archive and compression library URL:'
libart' Graphics routines used by the GnomeCanvas widget and some other applications. libart renders vector paths and the like.'
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:'
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:'
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:'
libconfig'Libconfig is a simple library for processing structured configuration files'
libConfuse' libConfuse is a configuration file parser library, licensed under the terms of the ISC license, and written in C.'
libctl'libctl is a free Guile-based library implementing flexible control files for scientific simulations. URL:'
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:'
libdrm'Direct Rendering Manager runtime library. URL:'
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:'
libelf'libelf is a free ELF object file access library URL:'
libepoxy'Epoxy is a library for handling OpenGL function pointer management for you URL:'
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:'
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:'
libffcall' GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters URL:'
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:'
libgcrypt'Libgpg-error is a small library that defines common error values for all GnuPG components. URL:'
libgd'GD is an open source code library for the dynamic creation of images by programmers. URL:'
libgeotiff'Library for reading and writing coordinate system information from/to GeoTIFF files URL:'
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:'
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:'
libglvnd'libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. URL:'
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:'
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:'
libgtextutils'ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream URL:'
libharu'libHaru is a free, cross platform, open source library for generating PDF files.'
libICE'X Inter-Client Exchange library for'
libiconv'Libiconv converts from one character encoding to another through Unicode conversion URL:'
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:'
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:'
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:'
libmatheval'GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. URL:'
libMemcached'libMemcached is an open source C/C-- client library and tools for the memcached server ( 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 ( URL:'
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:'
libnl' The libnl suite is a collection of libraries providing APIs to netlink protocol based Linux kernel interfaces. '
libpciaccess'Generic PCI access library. URL:'
libpng'libpng is the official PNG reference library URL:'
libpsl'C library for the Public Suffix List URL:'
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.'
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.'
libsamplerate'Secret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio. URL:'
libsigc++'The libsigc-- package implements a typesafe callback system for standard C--. URL:'
libsigsegv'GNU libsigsegv is a library for handling page faults in user mode. URL:'
libSM'X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.'
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:'
libsodium' Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. URL:'
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:'
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:'
LibTIFF'tiff: Library and tools for reading and writing TIFF data files URL:'
libtirpc'Libtirpc is a port of Suns Transport-Independent RPC library to Linux. URL:'
libtool'GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.'
libunistring' This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. URL:'
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:'
LibUUID'Portable uuid C library'
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:'
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:'
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:'
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.'
libXdamage'X Damage extension library'
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. '
libXext'Common X Extensions library'
libXfixes'X Fixes extension library'
libXfont'X font libary'
libXft'X11 client-side library'
libXi'LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.'
libXinerama'Xinerama multiple monitor library'
libxml++'libxml-- is a C-- wrapper for the libxml XML parser library. URL:'
libxml2' Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). URL:'
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:'
libXmu'libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. libXmuu is a lighter-weight version that does not depend on libXt or libXext'
libXp'libXp provides the X print library.'
libXpm'libXp provides the X print library.'
libXrandr'X Resize, Rotate and Reflection extension library'
libXrender'X11 client-side library'
libxslt'Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). URL:'
libxsmm'LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). URL:'
libXt'libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).'
libyaml'LibYAML is a YAML parser and emitter written in C. URL:'
libzeep' C-- library for reading and writing XML and creating web and SOAP servers'
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:'
LIGGGHTS-WITH-BONDS'LIGGGHTS® DEM software with Bonds enabled.'
Lighter'Fast and memory-efficient sequencing error corrector'
limix-bgen'A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. URL:'
LINKS' LINKS is a genomics application for scaffolding or re-scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It provides a generic framework for scaffolding and can work on any sequences. URL:'
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:'
LittleCMS' Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. URL:'
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:'
llvmlite'A lightweight LLVM python binding for writing JIT compilers URL:'
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:'
LMfit'Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python URL:'
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'
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:'
LongRanger'Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. There are five main pipelines, each triggered by a longranger command.'
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:'
lpsolve'Mixed Integer Linear Programming (MILP) solver'
L_RNA_scaffolder' L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments. The method is suitable for most genomes. The program could handle the transcript reads generated from 454/Sanger/Ion_Torrent sequencing, or de novo assembled with pair-end Illumina sequencing. Since the large introns cover most transcribed genome regions and RNA-sequencing is much less expensive than large insert library construction, the method provides a practical alternative to existing fosmid/BAC library_based approaches for scaffolding genome sequences in a cost effective way. '
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. URL:'
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:'
LTR_retriever' LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR-RT library for genome annotations. URL:'
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.'
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.'
LUMPY'A probabilistic framework for structural variant discovery.'
lwgrp' The Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups URL:'
lxml'The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
LYVE-SET(description not available)
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:'
LZO'Portable lossless data compression library URL:'
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:'
MACS' Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction.'
MACS2'Model Based Analysis for ChIP-Seq data URL:'
maeparser'maeparser is a parser for Schrodinger Maestro files. URL:'
MafFilter'MafFilter is a program dedicated to the analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files.'
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:'
mafTools'Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.'
Magic-BLAST' Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Unlike other BLAST nucleotide search programs, such as BLASTN or Megablast, Magic-BLAST produces spliced alignments and optimizes alignment scores for paired reads. URL:'
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.'
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:'
makedepend'The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. URL:'
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:'
Mako'A super-fast templating language that borrows the best ideas from the existing templating languages URL: 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. URL:'
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:'
MariaDB-connector-c'MariaDB Connector/C is used to connect applications developed in C/C-- to MariaDB and MySQL databases. URL:'
Markdown'Python implementation of Markdown.'
MarkupSafe'Python http for humans'
MARS'improving Multiple circular sequence Alignment using Refined Sequences URL:'
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). URL:'
MATCH'Multipurpose Atom Checker for CHARMM'
Math-Derivative' Math::Derivative - Numeric 1st and 2nd order differentiation URL:'
Math-Spline' Math::Spline - Cubic Spline Interpolation of data URL:'
Math-Utils' Math::Utils - Useful mathematical functions not in Perl. URL:'
MATIO'matio is an C library for reading and writing Matlab MAT files. URL:'
Matlab'A numerical computing environment and fourth-generation programming language.'
Matlab-MCR/products/compiler/mcr 'Matlab Component Runtime. standalone matlab libraries to run matlab codes.'
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:'
Mauve'Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. URL:'
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:'
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.'
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.'
Maxima' Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language.'
MBROLA''] ' 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: ['', '']'
mbuffer' mbuffer is a tool for buffering data streams with a large set of unique features. URL:'
McCortex'McCortex is a multi-sample de novo assembly and variant calling using Linked de bruijn graphs.'
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. '
mcOutbryk'mcOutbryk is a SNP calling pipeline using mccortex'
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.'
MDAnalysis'MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. URL:'
MDBM'MDBM is a super-fast memory-mapped key/value store URL:'
MDTraj'Read, write and analyze MD trajectories with only a few lines of Python code. URL:'
MECAT'MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads.'
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:'
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:'
Meep'Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. URL:'
MEGAHIT'An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
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:'
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: 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:'
meshio'meshio is a tool for reading/writing various mesh formats representing unstructured meshes URL:'
Meson'Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. URL:'
Mesquite'Mesh-Quality Improvement Library URL:'
MESS'Master Equation System Solver (MESS) URL:'
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:'
MetaCluster' MetaCluster5.0 is an unsupervised binning method that can (1) samples with low-abundance species, or (2) samples (even with high-abundance) with many extremely-low-abundance species.'
metaerg'MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline. URL:'
MetaEuk'MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics URL:'
MetaPhlAn'MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.'
MetaPhlAn2' MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0 MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species. '
MetaPlatanus' De novo assembly and sequence clustering of metagenomic data enable the construction ofmultiple draft genomes including those of uncultured organisms. URL:'
Metaxa2'Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically URL:'
MethPipe'The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS).'
MethylDackel'A (mostly) universal methylation extractor for BS-seq experiments. URL:'
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.'
MINC'Medical Image NetCDF or MINC isn't netCDF.'
MinCED'Mining CRISPRs in Environmental Datasets URL:'
Miniasm' Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.'
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:'
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:'
MiniScrub'MiniScrub is a de novo long sequencing read preprocessing method that improves read quality by predicting and removing ('scrubbing') read segments that have a high concentration of errors. Since long read technologies have high error rates, read scrubbing can be used to improve downstream applications such as alignment or assembly.'
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:'
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:'
miRDeep2' miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs '
miRhub'Candidate miRNA regulatory hub identification pipeline.'
misha'The misha package is intended to help users to efficiently analyze genomic data achieved from various experiments. URL:'
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:'
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:'
MITRE'MITRE learns predictive models of patient outcomes from microbiome time-series data in the form of short lists of interpretable rules URL:'
MiXCR' MiXCR processes big immunome data from raw sequences to quantitated clonotypes URL:'
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. 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:'
MMseqs2'MMseqs2: ultra fast and sensitive search and clustering suite URL:'
MOCAT2(description not available)
modtools' A tool set for manipulating MOD and pseudogenomes'
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:'
Mono'An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. URL:'
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.'
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:'
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.'
MotifMaker'MotifMaker is a tool for identify motifs associated with DNA modifications in prokaryotic genomes.'
motionSegmentation'Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. URL:'
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:'
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:'
MPFR' The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. URL:'
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: 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:'
mpifileutils' MPI-Based File Utilities For Distributed Systems URL:'
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:'
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:'
MrBayes'MrBayes is a program for the Bayesian estimation of phylogeny.'
MRCPP'MultiResolution Computation Program Package URL:'
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:'
msprime'msprime is a coalescent simulator and library for processing tree-based genetic data.'
Muave' Mauve is a software package that attempts to align orthologous and xenologous regions among two or more genome sequences that have undergone both local and large-scale changes.'
MultiNest'MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions. URL:'
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:'
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:'
MUMmer' MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. URL:'
mummichog'Mummichog is a Python program for analyzing data from high throughput, untargeted metabolomics. It leverages the organization of metabolic networks to predict functional activity directly from feature tables, bypassing metabolite identification.'
MUMPS'A parallel sparse direct solver URL:'
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. '
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:'
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:'
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:'
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: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
myHadoopSee sample job script, \$MYHADOOP_HOME/example/lsf.qsub 'myHadoop: wrapper for running Hadoop on HPC cluster'
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'
myriad'Simple distributed computing.'
MySQL-python'MySQL database connector for Python'
NAMD'NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. URL:'
NanoFilt'Filtering and trimming of Oxford Nanopore Sequencing data URL:'
nanoget'Functions to extract information from Oxford Nanopore sequencing data and alignments URL:'
nanomath'A few simple math function for other Oxford Nanopore processing scripts URL:'
Nanonet' Nanonet provides recurrent neural network basecalling for Oxford Nanopore MinION data. It represents the first generation of such a basecaller from Oxford Nanopore Technologies, and is provided as a technology demonstrator.'
NanoPlot'Plotting suite for long read sequencing data and alignments URL:'
nanopolish' A nanopore consensus algorithm using a signal-level hidden Markov model.'
NanoSim'NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology.'
NASM'NASM: General-purpose x86 assembler URL:'
NCBI-Toolkit'The NCBI Toolkit is a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services by the National Center for Biotechnology Information.'
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:'
NCCL'The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.'
ncdf4'ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files URL:'
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:'
NCL'NCL is an interpreted language designed specifically for scientific data analysis and visualization. URL:'
NCO'manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 URL:'
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:'
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:'
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:'
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:'
netcdf4-python'Python/numpy interface to netCDF. URL:'
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. '
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:'
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:'
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:'
networkx'NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. URL:'
NEURON'Empirically-based simulations of neurons and networks of neurons.'
NextDenovo'NextDenovo is a string graph-based de novo assembler for TGS long reads. URL:'
Nextflow'Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data URL:'
NextPolish'NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. URL:'
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:'
nglview'IPython widget to interactively view molecular structures and trajectories. URL:'
NGS'NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. URL:'
NGSadmix'NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods.'
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:'
NGS-Python'NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. URL:'
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:'
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:'
Nilearn'Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data. URL: 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:'
Ninja'Ninja is a small build system with a focus on speed. URL:'
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:'
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:'
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:'
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:'
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:'
nseg' nseg identifies and masks regions of low complexity in nucleic acid sequences. This distribution is a fork of nseg, modified to be more compliant with recent C compilers. URL:'
NSPR'Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. URL:'
NSS'Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. URL:'
ntEdit'ntEdit is a fast and scalable genomics application for polishing genome assembly drafts. URL:'
ntHits'ntHits is a method for identifying repeats in high-throughput DNA sequencing data. URL:'
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:'
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:'
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:'
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:'
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:'
Oases'Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.'
OBITools'The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of commands using the pipe mecanism.'
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:'
Octave'GNU Octave is a high-level interpreted language, primarily intended for numerical computations. URL:'
OMB'OSU (MPI) Micro-Benchmarks'
omniCLIP'omniCLIP is a Bayesian peak caller that can be applied to data from CLIP-Seq experiments to detect regulatory elements in RNAs. URL:'
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: URL:'
ont_albacore' Albacore performs real-time basecalls on Oxford Nanopore Technologies sequencing data.'
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:'
OpenAI-Gym'A toolkit for developing and comparing reinforcement learning algorithms. URL:'
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:'
OpenBLAS'OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. URL:'
openCARP'openCARP is an open cardiac electrophysiology simulator for in-silico experiments. URL:'
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:'
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:'
OpenEXR'OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications URL:'
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'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:'
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:'
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:'
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:'
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. '
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:'
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:'
OpenMolcas'OpenMolcas is a quantum chemistry software package URL:'
OpenMPI'The Open MPI Project is an open source MPI-3 implementation. URL:'
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:'
OpenPGM'OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at 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.'
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:'
openpyxl'A Python library to read/write Excel 2010 xlsx/xlsm files URL:'
OpenRefine'OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web. URL:'
OpenSees' The Open System for Earthquake Engineering Simulation (OpenSees) is a software framework for simulating the seismic response of structural and geotechnical systems. '
OpenSlide'OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). URL:'
openslide-python'OpenSlide Python is a Python interface to the OpenSlide library. URL: 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:'
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:'
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-HPRC-License'License terms for using ORCA on TAMU HPRC clusters'
OrfM'A simple and not slow open reading frame (ORF) caller.'
OrthoFinder'OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics URL:'
OrthoMCL' OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. '
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:'
OSPREY' OSPREY is a suite of programs for computational structure-based protein design.'
OSU-Micro-Benchmarks'OSU Micro-Benchmarks URL:'
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:'
OVITO' OVITO is a scientific visualization and analysis software for atomistic simulation data URL:'
p11-kit'Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process.'
P3DFFT' 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:'
p4vasp'Visualization suite for VASP'
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.'
PAGAN' PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions.'
PAGIT'Tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation. '
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:'
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:'
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:'
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:'
parallel'parallel: Build and execute shell commands in parallel URL:'
parallel-fastq-dump'parallel fastq-dump wrapper URL:'
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:'
ParaView'ParaView is a scientific parallel visualizer. URL:'
ParFlow' ParFlow is an integrated, parallel watershed model that makes use of high-performance computing to simulate surface and subsurface fluid flow. URL:'
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:'
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:'
Parsnp' Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees; both Parsnp and Gingr form part of the Harvest suite.'
PASA'PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. URL:'
Paste'Tools for using a Web Server Gateway Interface stack'
PasteDeploy'Load, configure, and compose WSGI applications and servers'
PasteScript'A pluggable command-line frontend, including commands to setup package file layouts'
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:'
patchelf'PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. URL:'' is a Python library implementing path objects as first-class entities, allowing common operations on files to be invoked on those path objects directly.'
PAUP'PAUP- (Phylogenetic Analysis Using Parsimony -and other methods) is a computational phylogenetics program for inferring evolutionary trees. URL:'
pauvre'Tools for plotting Oxford Nanopore and other long-read data URL:'
PBALIGN(description not available)
pbbam'The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices.'
PBSuite'Software for Long-Read Sequencing Data from PacBio URL:'
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.'
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:'
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:'
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:'
PeakRanger' PeakRanger: A multi-purpose ultrafast peak caller for ChIP Seq data '
PeakSplitter'Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks.'
PEAR'PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.'
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:'
Perl'Larry Wall's Practical Extraction and Report Language URL:'
PerlCyc' is a Perl module for accessing internal Pathway-Tools functions. URL:'
Perl_tamu' Perl_tamu contains perl modules that are not intalled in the easybuild module: GD GD::Graph GD::TextUtil PerlIO::gzip File::Spec::Link Parallel::ForkManager XML::NamespaceSupport XML::SAX XML::Lite XML::LibXML Array::Utils Exporter::Tiny List::MoreUtils Math::Counting CPAN::Meta inc::latest Module::Build Note: new modules may be added to the list when new modules are installed. '
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:'
petsc4py'petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.'
PGDSpider'An automated data conversion tool for connecting population genetics and genomics programs'
PGI'C, C-- and Fortran compilers from The Portland Group - PGI URL:'
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:'
PhiPack'The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well. URL:'
Phobius'Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. URL:'
phonopy'Phonopy is an open source package of phonon calculations based on the supercell approach. URL:'
PhyBin'PhyBin is a simple command line tool that classifies (bins) a set of Newick tree files by their topology. URL:'
PHYLIP'PHYLIP is a free package of programs for inferring phylogenies.'
PhyloBayes'A Bayesian software for phylogenetic reconstruction using mixture models URL:'
PhyloBayes-MPI'A Bayesian software for phylogenetic reconstruction using mixture models URL:'
phylokit'C-- library for high performance phylogenetics URL:'
phylonaut'Dynamic programming for phylogenetics applications URL:'
PhyloNetworks'PhyloNetworks is a Julia package for the manipulation, visualization, inference of phylogenetic networks, and their use for trait evolution.'
PhyloPhlAn' PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. URL:'
PhyloSNP'PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data.'
PhyML'Phylogenetic estimation using (Maximum) Likelihood URL:'
phyx'phyx performs phylogenetics analyses on trees and sequences. URL:'
picard'A set of tools (in Java) for working with next generation sequencing data in the BAM format. URL:'
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.'
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:'
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.'
Pillow'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. URL:'
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: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default)'
Pilon' Pilon is an automated genome assembly improvement and variant detection tool'
pip'The PyPA recommended tool for installing Python packages. URL:'
Piranha' Piranha is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. URL:'
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:'
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:'
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:'
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:'
PlanetWRF' The Planetary Weather Research and Forecasting model (planetWRF) is an open-source general purpose numerical model for planetary atmospheres research. '
PlantClusterFinder'A pipeline to predict metabolic gene clusters from plant genomes URL:'
PlasmaPy'Open source Python ecosystem for plasma research and education URL:'
Platanus'PLATform for Assembling NUcleotide Sequences'
Platanus_allee' Platanus-allee is a de novo haplotype assembler (phasing tool), which assembles each haplotype sequence in a diploid genome. URL:'
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:'
PLINK'plink-1.9-x86_64: Whole-genome association analysis toolset URL:'
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:''An open-source, interactive graphing library for Python URL: 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:'
PLY'PLY is yet another implementation of lex and yacc for Python.'
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:'
PnetCDF' PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (> 2B array elements).'
pocl'Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard URL:'
poetry'Python packaging and dependency management made easy URL:'
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:'
pompi'Toolchain with PGI C, C-- and Fortran compilers, alongside OpenMPI. URL:'
poppler'Poppler is a PDF rendering library based on the xpdf-3.0 code base. URL:'
popscle'A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools URL:'
POPT(description not available)
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:'
Poretools' A toolkit for working with nanopore sequencing data from Oxford Nanopore.'
Portcullis'Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites. In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user's own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it's portable). It then, analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Portcullis output's junctions in a variety of formats making it suitable for downstream analysis (such as differential splicing analysis and gene modelling) without additional work. Portcullis can also filter the original BAM file removing alignments associated with bad junctions. URL:'
PosiGene'PosiGene is a tool that (i) detects positively selected genes on genome-scale, (ii) allows analysis of specific evolutionary branches, (iii) can be used in arbitrary species contexts and (iv) offers visualization of the candidates.'
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.'
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.'
POTION' POTION (POsitive selecTION) is an open source, modular and end-to-end software for genomic scale detection of positive Darwinian selection in groups of homologous coding sequences through estimation of dN/dS ratios.'
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.'
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. URL:'
PRAP'PRAP is a platform independent Python3 tool used to analyze pan-resistome characteristics for multiple genomes. URL:'
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: 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.'
printproto' 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:'
P_RNA_scaffolder'P_RNA_scaffolder is a genome scaffolding tool with paired-end RNA-seq reads from studied species. URL:'
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.'
progressbar33'Text progress bar library for Python.'
ProgressiveCactus' Progressive Cactus is a whole-genome alignment package. '
PROJ'Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates URL:'
ProjectQ'An open source software framework for quantum computing'
prokka'Prokka is a software tool for the rapid annotation of prokaryotic genomes. URL:'
prompt-toolkit'prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.'
Proovread' Large-scale high accuracy PacBio correction through iterative short read consensus.'
protobuf'Google Protocol Buffers URL:'
protobuf-python'Python Protocol Buffers runtime library. URL:'
PRSice'PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. URL:'
PSCOM(description not available)
PSI4'PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.'
PsiCLASS'PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. URL:'
psmc'This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.'
PSMPI(description not available)
PSolver'Poisson Solver from the BigDFT code compiled as a standalone library.'
psrecord'psrecord is a small utility that uses the psutil library to record the CPU and memory activity of a process.'
PSSpred'PSSpred (Protein Secondary Structure prediction) is a simple neural network training algorithm for accurate protein secondary structure prediction. URL:'
pstoedit'pstoedit translates PostScript and PDF graphics into other vector formats'
psutil'A cross-platform process and system utilities module for Python URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
psycopg2' Psycopg is the most popular PostgreSQL adapter for the Python programming language.'
ptemcee'ptemcee, pronounced "tem-cee", is fork of Daniel Foreman-Mackey's wonderful emcee to implement parallel tempering more robustly. If you're trying to characterise awkward, multi-model probability distributions, then ptemcee is your friend. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
pubtcrs'This repository contains C-- source code for the TCR clustering and correlation analyses described in the manuscript "Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV and Philip Bradley, available on bioRxiv. URL:'
pullseq'Utility program for extracting sequences from a fasta/fastq file'
Purge_Dups'purge haplotigs and overlaps in an assembly based on read depth URL:'
Purge_Haplotigs'Pipeline to help with curating heterozygous diploid genome assemblies (for instance when assembling using FALCON or FALCON-unzip).'
py'library with cross-python path, ini-parsing, io, code, log facilities'
PyAPS3'Python 3 Atmospheric Phase Screen URL:'
pybedtools'pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
pyBigWig'A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
pybind11'pybind11 is a lightweight header-only library that exposes C-- types in Python and vice versa, mainly to create Python bindings of existing C-- code. URL:'
PyCairo'Python bindings for the cairo library URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
pycma'A stochastic numerical optimization algorithm for difficult (non-convex, ill-conditioned, multi-modal, rugged, noisy) optimization problems in continuous search spaces, implemented in Python. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
pycocotools'Official APIs for the MS-COCO dataset URL:'
PyCogent'PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.'
pycparser'C parser in Python'
PyCUDA' PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.'
pydicom'Pure python package for DICOM medical file reading and writing. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
pydot'Python interface to Graphviz's Dot language. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
Pydusa' Pydusa is a package for parallel programming using Python. It contains a module for doing MPI programming in Python. We have added parallel solver packages such as Parallel SuperLU for solving sparse linear systems.'
pyEGA3' A basic Python-based EGA download client URL:'
pyexcel_xlsx' pyexcel-xlsx is a tiny wrapper library to read, manipulate and write data in xlsx and xlsm fromat using openpyxl.'
pyfasta'Stores a flattened version of the fasta file without spaces or headers and uses either a mmap of numpy binary format or fseek/fread so the sequence data is never read into memory. URL:'
pyFFTW'A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
pyfits'The PyFITS module is a Python library providing access to FITS (Flexible Image Transport System)'
PyFMI'PyFMI is a package for loading and interacting with Functional Mock-Up Units (FMUs), which are compiled dynamic models compliant with the Functional Mock-Up Interface (FMI)'
PyGEOS'PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance improvement when operating on arrays of geometries. URL:'
Pygments'Pygments is a syntax highlighting package written in Python.'
PyGObject'PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. URL:'
pygraphviz'PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
pygrib'Python interface for reading and writing GRIB data URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
PyGTK' PyGTK lets you to easily create programs with a graphical user interface using the Python programming language.'
pyhdf'Python wrapper around the NCSA HDF version 4 library Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
pyiron'An integrated development environment (IDE) for computational materials science. URL:'
Pyke3'Pyke introduces a form of Logic Programming (inspired by Prolog) to the Python community by providing a knowledge-based inference engine (expert system) written in 100% Python.'
pylift' pylift is an uplift library that provides, primarily: (1) Fast uplift modeling implementations and (2) Evaluation tools (UpliftEval class). URL:'
Pylint'Pylint is a tool that checks for errors in Python code, tries to enforce a coding standard and looks for code smells. It can also look for certain type errors, it can recommend suggestions about how particular blocks can be refactored and can offer you details about the code's complexity. URL:'
py-lmdb' Universal Python binding for the LMDB 'Lightning' Database'
Pylons'Pylons Web Framework'
pymatgen' Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.'
PyMC3'Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano URL:'
PyNAST'PyNAST is a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rRNA sequences to existing 16s rRNA alignments. This reimplementation is more flexible, faster, and easier to install and maintain than the original NAST implementation.'
Pyomo' Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. '
PyOpenGL' PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.'
pyOpenSSL'High-level wrapper around a subset of the OpenSSL library.'
pyparsing'The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code. URL:'
PyPhlAn'Tools to use with GraPhlAn'
pyproj'Python interface to PROJ4 library for cartographic transformations URL:'
pyqi' pyqi (canonically pronounced pie chee) is a Python framework designed to support wrapping general commands in multiple types of interfaces, including at the command line, HTML, and API levels.'
PyQt'PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.'
PyQt5'PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.'
PyRAD' PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets. It uses a wrapper around an alignment-clustering algorithm, which allows for indel variation within and between samples, as well as for incomplete overlap among reads (e.g. paired-end) '
PyRe'PyRe (Python Reliability) is a Python module for structural reliability analysis. URL:'
PyRETIS'PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling. URL:'
Pyrex' Pyrex - a Language for Writing Python Extension Modules '
Pysam'Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
pyScaf'pyScaf orders contigs from genome assemblies utilising several types of information'
pySCENIC'pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data. URL:'
PySCF'PySCF is an open-source collection of electronic structure modules powered by Python. URL:'
pysndfx'A lightweight Python wrapper for SoX - Sound eXchange. Supported effects range from EQ and compression to phasers, reverb and pitch shifters. URL:'
pysnptools' PySnpTools is a library for reading and manipulating genetic data.'
pysqlite'pysqlite is an interface to the SQLite 3.x embedded relational database engine. It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.'
PyStan'Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.'
PyTables'PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. URL:'
pytest'pytest: simple powerful testing with Python URL:'
Python'Python is a programming language that lets you work more quickly and integrate your systems more effectively. URL:'
python-hl7'A simple library for parsing messages of Health Level 7 (HL7) version 2.x into Python objects. URL:'
python-hostlist' Python module for hostlist handling'
python-igraph'Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
python-Levenshtein'Python extension for computing string edit distances and similarities. URL:'
python-parasail'Python Bindings for the Parasail C Library URL:'
python-weka-wrapper3'Python3 wrapper for the Weka Machine Learning Workbench URL:'
pythran' Pythran is an ahead of time compiler for a subset of the Python language, with a focus on scientific computing. It takes a Python module annotated with a few interface description and turns it into a native Python module with the same interface, but (hopefully) faster. URL:'
PyTorch'Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. URL:'
PyVCF'A VCF parser for Python'
PyWavelets'PyWavelets is open source wavelet transform software for Python. URL:'
PyYAML'PyYAML is a YAML parser and emitter for the Python programming language. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0'
PyZMQ'Python bindings for ZeroMQ URL:'
Q6'EVB, FEP and LIE simulator. URL:'
QAPA'Analysis of alternative polyadenylation (APA) from RNA-seq data (human and mouse). URL:'
Qbox' Qbox is a C--/MPI scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism. Qbox is designed for operation on large parallel computers. URL:'
QCA' Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.'
qcat'qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files URL:'
qcint'libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform. URL:'
QDD'A user-friendly program to select microsatellite markers and design primers from large sequencing projects.'
QGIS' QGIS is a user friendly Open Source Geographic Information System (GIS)'
Qhull' Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. URL:'
Qiime'QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.'
QJson' QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa.'
qmd-progress' PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver. '
qpth' A fast and differentiable QP solver for PyTorch. URL:'
qrupdate'qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. URL:'
QScintilla' QScintilla is a port to Qt of Neil Hodgson's Scintilla C-- editor control'
QScintilla5' QScintilla is a port to Qt of Neil Hodgson's Scintilla C-- editor control'
Qt'Qt is a comprehensive cross-platform C-- application framework.'
Qt5'Qt is a comprehensive cross-platform C-- application framework. URL:'
Quake' Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. '
Qualimap'Qualimap examines sequencing alignment data in SAM/BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.'
QuantumESPRESSO'Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). URL:'
QUAST'QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison.'
QuaZIP'QuaZIP is the C-- wrapper for Gilles Vollant's ZIP/UNZIP package (AKA Minizip) using Trolltech's Qt library. URL:'
QuickFF'QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations. URL:'
QuTiP'QuTiP is open-source software for simulating the dynamics of open quantum systems.'
Qwt'The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. URL:'
QwtPolar' The QwtPolar library contains classes for displaying values on a polar coordinate system.'
R'R is a free software environment for statistical computing and graphics. URL:'
R6'Classes with Reference Semantics'
Racon'Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. URL:'
RaGOO' A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome. URL:'
Ragout'Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references. Given a set of assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds). URL:'
rainbow'Efficient tool for clustering and assembling short reads, especially for RAD.'
randfold'Minimum free energy of folding randomization test software'
RapidJSON'A fast JSON parser/generator for C-- with both SAX/DOM style API URL:'
rasterio'Rasterio reads and writes geospatial raster data. URL:'
rasterstats'rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries. URL:'
RAxML'RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. URL:'
RAxML-NG'RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. URL:'
RBFOpt'RBFOpt is a Python library for black-box optimization (also known as derivative-free optimization). URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
R-bundle-Bioconductor'Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. URL:'
rclone' Rclone is a command line program to sync files and directories to and from a variety of online storage services URL:'
RColorBrewer'ColorBrewer Palettes'
Rcpp, 'Seamless R and C-- Integration'
RDFlib'RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information. URL: Compatible modules: Python/2.7.16-GCCcore-8.3.0 (default), Python/3.7.4-GCCcore-8.3.0'
re2c're2c is a free and open-source lexer generator for C and C--. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. URL:'
REAPR'REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.'
RECON' RECON: a package for automated de novo identification of repeat families from genomic sequences. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. URL:'
Red'Red (REpeat Detector) URL:'
Redundans'Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.'
RegTools'Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. URL:'
RELION'RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).'
REMORA'REsource MOnitoring for Remote Applications URL:'
renderproto'Xrender protocol and ancillary headers'
RepeatExplorer2'RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes. URL:'
RepeatMasker'RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. URL:'
RepeatModeler'RepeatModeler is a de novo transposable element (TE) family identification and modeling package. URL:'
RepeatScout'RepeatScout is a tool to discover repetitive substrings in DNA. The purpose of the RepeatScout software is to identify repeat familysequences from genomes where hand-curated repeat databases (a la RepBase update) are not available. In fact, the output of this program can be used as input to RepeatMasker as a way of automatically masking newly-sequenced genomes.. URL:'
requests'Python http for humans'
reshape2'Flexibly Reshape Data: A Reboot of the Reshape Package.'
rgeos'R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries URL:'
rickflow'Running and Analyzing OpenMM Jobs URL:'
rioxarray'geospatial xarray extension powered by rasterio URL:'
rjags'The rjags package is an interface to the JAGS library. URL:'
rMATS'MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. URL:'
rmats2sashimiplot'rmats2sashimiplot produces a sashimiplot visualization of rMATS output. rmats2sashimiplot can also produce plots using an annotation file and genomic coordinates. The plotting backend is MISO. URL:'
RMBlast'RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. URL:'
RNAclust'RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file.'
RNAFramework'RNA Framework is a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data. URL:'
RNAIndel'RNAIndel calls coding indels and classifies them into somatic, germline, and artifact from tumor RNA-Seq data.'
RNAmmer' RNAmmer predicts ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models: An initial spotter model searches both strands. The spotter model is constructed from highly conserved loci within a structural alignment of known rRNA sequences. Once the spotter model detects an approximate position of a gene, flanking regions are extracted and parsed to the full model which matches the entire gene. By enabling a two-level approach it is avoided to run a full model through an entire genome sequence allowing faster predictions.'
RNA-SeQC'RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.'
rnaseqtools'rnaseqtools provides a set of tools to process transcripts (mainly in gtf format). URL:'
Roary'Rapid large-scale prokaryote pan genome analysis URL:'
ROOT'The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. URL:'
root_numpy'root_numpy is a Python extension module that provides an efficient interface between ROOT and NumPy. root_numpy’s internals are compiled C-- and can therefore handle large amounts of data much faster than equivalent pure Python implementations. URL:'
rootpy'The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate your data and to take advantage of these alternatives if needed. URL:'
Rosetta'Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.'
rpy2'rpy2 is an interface to R running embedded in a Python process. URL:'
RSAT'Regulatory Sequence Analysis Tools (RSAT), a software suite for the detection of cis-regulatory elements in genomic sequences.'
RSEM'RNA-Seq by Expectation-Maximization'
RSeQC'RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. URL:'
rstanarm'Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C-- library for Bayesian estimation. URL:'
rstudio'This RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) URL:'
R_tamu'R is a free software environment for statistical computing and graphics.'
RTG-Tools' RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats. URL:'
Ruby'Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. URL:'
Rust'Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. URL:'
S4' S4 (or simply S4) stands for Stanford Stratified Structure Solver, a frequency domain code to solve the linear Maxwell’s equations in layered periodic structures. Internally, it uses Rigorous Coupled Wave Analysis (RCWA; also called the Fourier Modal Method (FMM)) and the S-matrix algorithm.'
SaguaroGW'Saguaro Genome-Wide is a program to detect signatures of selection within populations, strains, or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in the genome. URL:'
Sailfish'Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads. URL:'
SalmID'Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia). URL:'
Salmon'Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. URL:'
SalmonTools'This repository contains (or will contain) a suite of tools that are useful for working with Salmon output. URL:'
SALSA'A tool to scaffold long read assemblies with Hi-C URL:'
Sambamba'Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth'
samblaster'samblaster: a tool to mark duplicates and extract discordant and split reads from sam files URL:'
samclip'Filter SAM file for soft and hard clipped alignments'
SAMtools'SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. URL:'
SAS' a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics. '
SAVI'Semi-Automated Validation Infrastructure (SAVI) processes predicted metabolic pathways using pathway meta data suc h as taxonomic distribution and key reactions and makes decisions about which pathways to keep, remove, or subject to manual valida tion. URL:'
savvy'Interface to various variant calling formats. URL:'
Saxon-HE'Open Source SAXON XSLT processor developed by Saxonica Limited. URL:'
ScaFaCoS'ScaFaCoS is a library of scalable fast coulomb solvers. URL:'
ScaLAPACK'The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. URL:'
Scalasca' Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes. URL:'
scales'Scale Functions for Visualization'
SCATS'A statistical tool to detect differential alternative splicing events using single-cell RNA-seq URL:'
ScientificPython'ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.'
scikit-allel'This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries. URL:'
scikit-build'Scikit-Build, or skbuild, is an improved build system generator for CPython C/C--/Fortran/Cython extensions. URL:'
scikit-image'scikit-image is a collection of algorithms for image processing. URL:'
scikit-learn'Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. URL:'
scikit-optimize'Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. URL:'
SCIPhI'Single-cell mutation identification via phylogenetic inference (SCIPhI) is a new approach to mutation detection in individual tumor cells by leveraging the evolutionary relationship among cells.'
scipy'SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python. URL:'
SciPy-bundle'Bundle of Python packages for scientific software URL:'
SCons'SCons is a software construction tool. URL:'
SCOOP'SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
Score-P' The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. URL:'
SCOTCH'Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. URL:'
scp'The module uses a paramiko transport to send and recieve files via the scp1 protocol.'
Scripture' Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. '
scVelo'scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling. URL:'
Scythe' Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. URL:'
SDA'Segmental Duplication Assembler'
SDL2'SDL: Simple DirectMedia Layer, a cross-platform multimedia library URL:'
SDSL'The Succinct Data Structure Library (SDSL) is a powerful and flexible C--11 library implementing succinct data structures. URL:'
sdsl-lite'Succinct Data Structure Library 2.0 URL:'
Seaborn' Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. URL:'
SECAPR'SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments URL:'
Seeder' Seeder is a framework for DNA motif discovery. URL:'
segemehl'segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. URL:'
SeisSol' SeisSol is a software package for simulating wave propagation and dynamic rupture based on the arbitrary high-order accurate derivative discontinuous Galerkin method (ADER-DG).'
SentencePiece'Unsupervised text tokenizer for Neural Network-based text generation. URL:'
sep'Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only)'
SEPP'SEPP stands for 'SATe-enabled Phylogenetic Placement', and addresses the problem of phylogenetic placement of short reads into reference alignments and trees. URL:'
SeqAn'SeqAn is an open source C-- library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data'
SeqKit' A cross-platform ultrafast comprehensive toolkit for FASTA/Q processing'
Seqmagick'We often have to convert between sequence formats and do little tasks on them, and it's not worth writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.'
seqOutBias' Molecular biology enzymes have nucleic acid preferences for their substrates; the preference of an enzyme is typically dictated by the sequence at or near the active site of the enzyme. This bias may result in spurious read count patterns when used to interpret high-resolution molecular genomics data. The seqOutBias program aims to correct this issue by scaling the aligned read counts by the ratio of genome-wide observed read counts to the expected sequence based counts for each k-mer.'
SeqPrep'Tool for stripping adaptors and/or merging paired reads with overlap into single reads.'
SeqSero' Salmonella serotyping from genome sequencing data. SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.'
SeqSero2' Salmonella serotyping from genome sequencing data. SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. URL:'
Seqtk' Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.'
Serf'The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library URL:'
setuptools' Download, build, install, upgrade, and uninstall Python packages -- easily!'
SHAP'SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions. URL:'
SHAPEIT'SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. The version 4 is a refactored and improved version of the SHAPEIT algorithm with multiple key additional features'
SHAPEIT4' SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. URL:'
Shapely'Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. URL:'
shrinkwrap'A std::streambuf wrapper for compression formats. URL:'
Sibelia'Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.'
SICER'A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.'
SICER2'Redesigned and improved ChIP-seq broad peak calling tool SICER URL:'
Siesta'SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.'
SignalP'SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.'
Silo' Silo is a library for reading and writing a wide variety of scientific data to binary, disk files'
simMSG'Exact numerical calculation of the joint site-frequency spectrum as in Wakeley and Hey (1997) Estimating ancestral population parameters. URL:'
SimpleElastix'Multi-lingual medical image registration library. URL:'
SimpleITK'imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance. URL:'
simplejson'Simple, fast, extensible JSON encoder/decoder for Python'
simpy'SimPy is a process-based discrete-event simulation framework based on standard Python. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
SIONlib' SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. URL:'
SIP'SIP is a tool that makes it very easy to create Python bindings for C and C-- libraries.'
sistr_cmd'Salmonella In Silico Typing Resource (SISTR) commandline tool URL:'
six'Python 2 and 3 compatibility utilities'
SKESA'SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.'
SLATEC'SLATEC Common Mathematical Library, a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77. URL:'
SLEPc'SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. URL:'
slepc4py'Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations.'
slidingwindow'slidingwindow is a simple little Python library for computing a set of windows into a larger dataset, designed for use with image-processing algorithms that utilise a sliding window to break the processing up into a series of smaller chunks.'
SLR'SLR is a scaffolding tool based on long reads and contig classification. URL:'
SMALT'SMALT efficiently aligns DNA sequencing reads with a reference genome.'
Smartie-sv'Smartie-sv will align query contigs against a reference genome and call structural variants. URL:'
snakemake'The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. URL:'
SNAP'SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.'
SNAP-HMM'(Semi-HMM-based Nucleic Acid Parser) gene prediction tool'
snappy'Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. URL:'
Sniffles' Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp-) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.'
Snoscan'Search for C/D box methylation guide snoRNA genes in a genomic sequences URL:'
snpEff'SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). URL:'
SNPGenie'SNPGenie is a collection of Perl scripts for estimating πN/πS, dN/dS, and other evolutionary parameters from next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data.'
SNPhylo'SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data URL:'
SNPomatic'High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient, and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping.'
SNP-Pipeline'The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.'
SNP-sites'Rapidly extracts SNPs from a multi-FASTA alignment. URL:'
SOAPdenovo2'SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.'
SOAPfuse'SOAPfuse is an open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data.'
socat'socat is a relay for bidirectional data transfer between two independent data channels. URL:'
SOFI2D' SOFI2D stands for Seismic mOdeling with FInite differences and denotes our 2D viscoelastic time domain massive parallel modeling code for P- and SV-waves. SOFI2D is the forward solver for the full waveform inversion code IFOS2D.'
sonic' Sonic is a simple algorithm for speeding up or slowing down speech. However, it's optimized for speed ups of over 2X, unlike previous algorithms for changing speech rate. The Sonic library is a very simple ANSI C library that is designed to easily be integrated into streaming voice applications, like TTS back ends. URL:'
SoX'SoX is the Swiss Army Knife of sound processing utilities. It can convert audio files to other popular audio file types and also apply sound effects and filters during the conversion. URL:'
SPAdes'Genome assembler for single-cell and isolates data sets URL:'
spaln'Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. URL:'
Spark'Spark is Hadoop MapReduce done in memory URL:'
sparsehash' An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. URL:'
SPECFEM2D' SPECFEM2D simulates forward and adjoint seismic wave propagation in two-dimensional acoustic, (an)elastic, poroelastic or coupled acoustic-(an)elastic-poroelastic media, with Convolution PML absorbing conditions.'
SpeedSeq'A flexible framework for rapid genome analysis and interpretation.'
spglib'Spglib is a C library for finding and handling crystal symmetries.'
spglib-python'Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. URL:'
Sphinx'Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C-- is already supported as well, and it is planned to add special support for other languages as well.'
sphire'SParx for HIgh Resolution Electron Microscopy'
Spine'Spine is a program for identification of the conserved core genome of bacteria and other small genome organisms. URL:'
SplAdder' Splicing Adder is a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data. URL:'
SPLASH'SPLASH is a free and open source visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations.'
SpliceMap'SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths. URL:'
Spyder'Spyder is an interactive Python development environment providing MATLAB-like features in a simple and light-weighted software. URL:'
SQLAlchemy' SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL.'
SQLite'SQLite: SQL Database Engine in a C Library URL:'
SRA-Toolkit'The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format URL:'
SRNANALYZER(description not available)
SRPRISM'Single Read Paired Read Indel Substitution Minimizer URL:'
SRST2' Short Read Sequence Typing for Bacterial Pathogens -- This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. URL:'
SSPACE_Basic'SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension'
SSPACE-LongRead' SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format. '
SSPACE-STANDARD' SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format. '
Stacks'Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. URL:'
STAMP-METAGENOMICS' STAMP is a software package for analyzing taxonomic or metabolic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. Statistical hypothesis tests for pairs of samples or groups of samples is support along with a wide range of exploratory plots.'
Stampy'Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. URL:'
STAR'STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. URL:'
STAR-CCM+'Software for solving problems involving flow (of fluids or solids), heat transfer and stress.'
STAR-Fusion' STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. URL:'
STAR-STAR'Spliced Transcripts Alignment to a Reference'
Statistics-R'Perl interface with the R statistical program URL:'
statsmodels'Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. URL:'
stpipeline'The ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format to generated datasets for down-stream analysis. The ST pipeline can also be used to process single cell data as long as a file with barcodes identifying each cell is provided. The ST Pipeline can also process RNA-Seq datasets generated with or without UMIs. URL:'
STREAM'The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.'
strelka'Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.'
stringi 'Character String Processing Facilities'
stringr'Simple, Consistent Wrappers for Common String Operations'
StringTie'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts URL:'
Structure'The program structure is a free software package for using multi-locus genotype data to investigate population structure. URL:'
Structure_threader'A program to parallelize the runs of Structure, fastStructure and MavericK software. URL:'
Subread'High performance read alignment, quantification and mutation discovery URL:'
Subversion' Subversion is an open source version control system.'
SuiteSparse'SuiteSparse is a collection of libraries manipulate sparse matrices. URL:'
SUMO' "Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation. URL:'
SUNDIALS'SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers URL:'
SunPy'The community-developed, free and open-source solar data analysis environment for Python. URL:'
SuperLU' SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.'
SuperLU_DIST' SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.'
supermagic'Very simple MPI sanity code. Nothing more, nothing less. URL:'
suspenders' Allows the merging of alignments that have been annotated using pylapels into a single alignment that picks the highest quality alignment.'
SVDetect'SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identifying structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.'
SVDquest'SVDquartets-based species trees URL:'
SVG'Perl binding for SVG URL:'
svtyper'Bayesian genotyper for structural variants'
swak4Foam' swak4Foam stands for SWiss Army Knife for Foam. Like that knife it rarely is the best tool for any given task, but sometimes it is more convenient to get it out of your pocket than going to the tool-shed to get the chain-saw. '
swalign' This package implements a Smith-Waterman style local alignment algorithm. You can align a query sequence to a reference. The scoring functions can be based on a matrix, or simple identity.'
SWAN' SWAN is a third-generation wave model, developed at Delft University of Technology, that computes random, short-crested wind-generated waves in coastal regions and inland waters. '
SWAT+' The Soil & Water Assessment Tool (SWAT) is a small watershed to river basin-scale model used to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. In order to face present and future challenges in water resources modeling SWAT code has undergone major modifications over the past few years, resulting in SWAT-, a completely revised version of the model. SWAT- provides a more flexible spatial representation of interactions and processes within a watershed. URL:'
SWIG'SWIG is a software development tool that connects programs written in C and C-- with a variety of high-level programming languages. URL:'
swissknife'Perl module for reading and writing UniProtKB data in plain text format. URL:'
SymEngine'SymEngine is a standalone fast C-- symbolic manipulation library. URL:'
sympy'SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. URL:'
Szip' Szip compression software, providing lossless compression of scientific data URL:'
tabix' Generic indexer for TAB-delimited genome position files '
TagLib'TagLib is a library for reading and editing the meta-data of several popular audio formats. URL:'
Tahoe' Tahoe is an open source research-oriented software platform for the development of numerical methods and material models. URL:'
TAMkin'TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry and reaction kinetics. It uses a Hessian computation from a standard computational chemistry program as its input. URL:'
tamu-libs'This module provides missing libraries for compute nodes.'
TandemTools'TandemTools package includes TandemQUAST tool for evaluating and improving assemblies of extra-long tandem repeats (ETR) and TandemMapper tool for mapping long error-prone reads to ETRs. URL:'
TargetFinder'Plant small RNA target prediction tool URL:'
TASSEL' TASSEL provides tools to investigate relationships between phenotypes and genotypes'
tbb'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. URL:'
tbl2asn'Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank URL:'
Tcl' Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. URL:'
TCLAP'TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary. URL:'
tcsh'Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. URL:'
Tecplot'Tecplot for CONVERGE URL:'
Tecplot360EX' Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, and communicate your results with professional images and animations. URL:'
Telescope'Single locus resolution of Transposable ELEment expression using next-generation sequencing. URL:'
TensorFlow'An open-source software library for Machine Intelligence'
terminaltables' Generate simple tables in terminals from a nested list of strings.'
tesseract'Tesseract is an optical character recognition engine'
testfixtures'Testfixtures is a collection of helpers and mock objects that are useful when writing automated tests in Python.'
testpath'Test utilities for code working with files and commands'
TetGen' A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator '
texinfo'Texinfo is the official documentation format of the GNU project. URL:'
Theano'Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. URL:'
thirdorder' The purpose of the thirdorder scripts is to help users of [ShengBTE] ( create FORCE_CONSTANTS_3RD files in an efficient and convenient manner.'
TiCCutils'TiCC utils is a collection of generic C-- software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.'
tidybayes' Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. URL:'
tidymodels'The tidy modeling "verse" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse. URL:'
TiMBL'TiMBL (Tilburg Memory Based Learner) is an open source software package implementing several memory-based learning algorithms, among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in common that they store some representation of the training set explicitly in memory. During testing, new cases are classified by extrapolation from the most similar stored cases.'
time'The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running. URL:'
TINKER'The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. URL:'
TinyDB'TinyDB is a lightweight document oriented database optimized for your happiness :) It's written in pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an external database server. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0'
Tk'Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. URL:'
Tkinter'Tkinter module, built with the Python buildsystem URL:'
TM-align'This package unifies protein structure alignment and RNA structure alignment into the standard TM-align program for single chain structure alignment, MM-align program for multi-chain structure alignment, and TM-score program for sequence dependent structure superposition. URL:'
TMHMM'Prediction of transmembrane helices in proteins.'
tmux'tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.'
ToFu'Tomography for Fusion. URL:'
Togl'A Tcl/Tk widget for OpenGL rendering. URL:'
Tombo'Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data. URL:'
TopHat'TopHat is a fast splice junction mapper for RNA-Seq reads. URL:'
torchvision' Datasets, Transforms and Models specific to Computer Vision URL:'
ToscaWidgets'Web widget creation toolkit based on TurboGears widgets'
tqdm'A fast, extensible progress bar for Python and CLI URL: Compatible modules: Python/2.7.18-GCCcore-9.3.0 (default), Python/3.8.2-GCCcore-9.3.0'
TransDecoder'TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.'
Transrate' nsrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.'
TreeMix'TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.'
treePL' treePL is a phylogenetic penalized likelihood program. URL:'
trf'Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. There is no need to specify the pattern, the size of the pattern or any other parameter.'
Trilinos'The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.'
trimAl'A tool for automated alignment trimming in large-scale phylogenetic analyses URL:'
Trim_Galore'Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. URL:'
Trimmomatic'Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. URL:'
Trinity'Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. URL:'
Trinity_tamu'Trinity tamu is a utility on top of Trinity, developed at HPRC. It adds additional flags to Trinity to enable use of multiple nodes to run some parts of Trtinity. '
Trinotate'Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST-/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases).'
tRNAscan-SE' Searching for tRNA genes in genomic sequences URL:'
Trycycler'Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. URL:'
TurboCheetah'TurboGears plugin to support use of Cheetah templates'
TurboJson'Python template plugin that supports JSON'
UCLUST'UCLUST: Extreme high-speed sequence clustering, alignment and database search.'
UCSCtools' UCSC utilities pre-compiled binaries. '
UCX'Unified Communication X An open-source production grade communication framework for data centric and high-performance applications URL:'
UDUNITS'UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.'
UFL'The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation.'
umi4cPackage'umi4cPackage is a processing and analysis pipeline for UMI-4C experiment. URL:'
umis'Package for estimating UMI counts in Transcript Tag Counting data. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0'
UMI-tools'Tools for handling Unique Molecular Identifiers in NGS data sets URL:'
Unblur' Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion.'
Unicycler'Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm-Racon pipeline.'
unrar'RAR is a powerful archive manager.'
UnZip'UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality. URL:'
USEARCH'USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST. URL:'
utf8proc'utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. URL:'
util-linux'Set of Linux utilities URL:'
Valgrind'Valgrind: Debugging and profiling tools URL:'
VarScan'Variant calling and somatic mutation/CNV detection for next-generation sequencing data URL:'
vawk' An awk-like VCF parser. vawk command syntax is exactly the same as awk syntax with a few additional features.'
VCF-kit'VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files. URL:'
vcflib' A C-- library for parsing and manipulating VCF files. '
VCFtools'The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.'
vContact2'vConTACT2 is a tool to perform guilt-by-contig-association automatic classification of viral contigs. URL:'
Velvet'Sequence assembler for very short reads'
VelvetOptimiser'VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.'
VEP'Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.'
version_required'A TAMU HPRC module to force users to specify a version when loading certain modules'
ViennaRNA'The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.'
Vim' Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. URL:'
viridisLite'Default Color Maps from 'matplotlib' (Lite Version)'
VisIt' VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.'
Vmatch' Large scale sequence analysis software.'
VMD' VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.'
Voro++'Voro-- is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro-- library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. URL:'
VSEARCH' VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. URL:'
V_Sim' V_Sim visualizes atomic structures such as crystals, grain boundaries and so on (sic)'
VTK'The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C-- class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. URL:'
VTune'Intel VTune Amplifier XE is the premier performance profiler for C, C--, C#, Fortran, Assembly and Java.'
WCT' NOAA's Weather and Climate Toolkit (WCT) is free, platform independent software distributed from NOAA's National Centers for Environmental Information (NCEI). The WCT allows the visualization and data export of weather and climate data, including Radar, Satellite and Model data. The WCT also provides access to weather/climate web services provided from NCEI and other organizations. URL:'
wcwidth'wcwidth is a low-level Python library to simplify Terminal emulation.'
WEBPROXY(description not available)
WebSocket++' WebSocket-- is an open source (BSD license) header only C-- library that implements RFC6455 The WebSocket Protocol. URL:'
Werkzeug' The Swiss Army knife of Python web development'
Westmere'Westmere (large-memory node) built packages for'
wget'pure python download utility'
WGS'Celera Assembler : scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999.'
WhatsHap' WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. URL:'
wheel'A built-package format for Python.'
wise2'wise2 key programs are genewise, a program for aligning proteins or protein HMMs to DNA, and dynamite a rather cranky "macro language" which automates the production of dynamic programming. '
worker'The Worker framework has been developed to help deal with parameter exploration experiments that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also URL:'
WPS'WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. URL:'
WRF'The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. URL:'
wrf-deps'This module sets up dependency requirements for building customized WRF.'
wtdbg2' Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. URL:'
wxPython' wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C--.'
X11'The X Window System (X11) is a windowing system for bitmap displays URL:'
x264' x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. URL:'
x265' x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. URL:'
xarray'xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. URL:'
xbitmaps'provides bitmaps for x'
xcb-proto'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.'
XCfun' XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals. URL:'
XCrySDen'XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. URL:'
Xerces-C++'Xerces-C-- is a validating XML parser written in a portable subset of C--. Xerces-C-- makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. URL:'
xextproto'XExtProto protocol headers.'
XFOIL' XFOIL is an interactive program for the design and analysis of subsonic isolated airfoils.'
XGBoost'XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. URL:'
XIOS' XIOS, or XML-IO-Server, is a library dedicated to I/O management in climate codes. XIOS manages output of diagnostics and other data produced by climate component codes into files and offers temporal and spatial post-processing operations on this data. URL:'
xlrd' Library for developers to extract data from Microsoft Excel (tm) spreadsheet files'
XlsxWriter'A Python module for creating Excel XLSX files'
XMDS2' The purpose of XMDS2 is to simplify the process of creating simulations that solve systems of initial-value first-order partial and ordinary differential equations.'
XML-LibXML'Perl binding for libxml2 URL:'
XML-Lite'A lightweight XML parser for simple files URL:'
XML-Parser'This is a Perl extension interface to James Clark's XML parser, expat.'
xorg-macros' macros utilities. URL:'
xprop'The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. URL:'
xproto'X protocol and ancillary headers URL:'
XSD'CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C-- data binding compiler. URL:'
xssp' The source code for building the mkdssp, mkhssp, hsspconv, and hsspsoap programs is bundled in the xssp project. The DSSP executable is mkdssp.'
xtrans'xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. '
XZ'xz: XZ utilities URL:'
yaff'Yaff stands for 'Yet another force field'. It is a pythonic force-field code. URL:'
yaml-cpp' yaml-cpp is a YAML parser and emitter in C-- matching the YAML 1.2 spec.'
Yasm'Yasm: Complete rewrite of the NASM assembler with BSD license'
YAXT'Yet Another eXchange Tool URL:'
zarr'Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. URL:'
ZDOCK'Protein docking sotware that performs a full rigid-body search of docking orientations between two proteins'
ZeroMQ'ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. URL:'
Zip'Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality URL:'
zlib' zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. URL:'
zsh'Zsh is a shell designed for interactive use, although it is also a powerful scripting language. URL:'
zstd'Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. URL:'