Software Modules on the Grace Cluster

Last Updated: Jul 9 09:33:55 CDT

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

Name Description
4ti2'A software package for algebraic, geometric and combinatorial problems on linear spaces'
AAF'AAF constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment.'
ABAQUS'Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.'
ABINIT'ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.'
ABRicate'Mass screening of contigs for antimicrobial and virulence genes'
ABySS'Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler'
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.'
ADIOS'The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.'
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. '
AGFusion'AGFusion is a python package for annotating gene fusions from the human or mouse genomes.'
aiohttp'" Async http client/server framework '
ALFA'ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.'
Amara'Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML.'
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'
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. '
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. '
angsd'Program for analysing NGS data.'
Annif'Annif is a multi-algorithm automated subject indexing tool for libraries, archives and museums.'
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. '
AnsysEM'Ansys electromagnetic field simulation helps you design innovative electrical and electronic products faster and more cost-effectively. '
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.'
antiSMASH'antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.'
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.'
anvio'An analysis and visualization platform for 'omics data.'
any2fasta'Convert various sequence formats to FASTA'
apex'A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch'
APR'Apache Portable Runtime (APR) libraries.'
APR-util'Apache Portable Runtime (APR) util libraries.'
ARAGORN'a program to detect tRNA genes and tmRNA genes in nucleotide sequences'
Arb'Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested.'
arcasHLA'arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.'
archspec'A library for detecting, labeling, and reasoning about microarchitectures'
ARGoS'A parallel, multi-engine simulator for heterogeneous swarm robotics'
argtable'Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. '
Arlequin'Arlequin: An Integrated Software for Population Genetics Data Analysis'
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.'
arpack-ng'ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.'
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.'
arrow'R interface to the Apache Arrow C++ library'
Arrow'Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform for in-memory data.'
ArviZ'Exploratory analysis of Bayesian models with Python'
ASAP3'ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE).'
ASE'ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.'
Assimulo'Assimulo is a simulation package for solving ordinary differential equations.'
ASTRID'ASTRID-2 is a method for estimating species trees from gene trees.'
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.'
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. '
AtomPAW'AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library.'
at-spi2-atk'AT-SPI 2 toolkit bridge '
at-spi2-core'Assistive Technology Service Provider Interface. '
attr'Commands for Manipulating Filesystem Extended Attributes'
augur'Pipeline components for real-time phylodynamic analysis'
AUGUSTUS'AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences'
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_Vina'AutoDock Vina is an open-source program for doing molecular docking. '
Automake'Automake: GNU Standards-compliant Makefile generator'
AutoMap'Tool to find regions of homozygosity (ROHs) from sequencing data.'
Autotools'This bundle collect the standard GNU build tools: Autoconf, Automake and libtool '
awscli'Universal Command Line Environment for AWS'
Bader'A fast algorithm for doing Bader's analysis on a charge density grid.'
bam-readcount'Count DNA sequence reads in BAM files'
BamTools'BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.'
barrnap'Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes.'
basemap'The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python'
BatMeth2'An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.'
Bazel'Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.'
BBMap'BBMap short read aligner, and other bioinformatic tools.'
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'
bcl2fastq2'bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.'
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.'
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. '
BeautifulSoup'Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.'
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'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.'
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.'
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.'
BinSanity'BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes.'
binutils'binutils: GNU binary utilities'
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'
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. '
Bio-EUtilities'BioPerl low-level API for retrieving and storing data from NCBI eUtils'
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.'
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. '
BioServices'Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).'
Bismark'A tool to map bisulfite converted sequence reads and determine cytosine methylation states'
Bison'Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.'
bitarray'bitarray provides an object type which efficiently represents an array of booleans'
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.'
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.'
BLIS'AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.'
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'
bmtagger'Best Match Tagger for removing human reads from metagenomics datasets'
bokeh'Statistical and novel interactive HTML plots for Python'
Bonito'Convolution Basecaller for Oxford Nanopore Reads'
Boost'Boost provides free peer-reviewed portable C++ source libraries.'
Boost.Python'Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.'
Bottleneck'Fast NumPy array functions written in C'
Bowtie'Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.'
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.'
BRAKER'BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.'
breseq'breseq is a computational pipeline for the analysis of short-read re-sequencing data'
BSMAPz'Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study.'
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>'
BUSCO'BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs'
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.'
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.'
bwidget'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.'
bx-python'The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.'
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. '
C3D'Convert3D Medical Image Processing Tool'
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'
cairomm'The Cairomm package provides a C++ interface to Cairo.'
Calendrical'Calendrical module is for calendrical calculations.'
canu'Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing'
CapnProto'Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.'
carputils'carputils is a Python framework for generating and running openCARP examples.'
Cartopy'Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.'
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. '
causallift'CausalLift: Python package for Uplift Modeling in real-world business; applicable for both A/B testing and observational data '
causalml'Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML '
CAVIAR'CAusal Variants Identication in Associated Regions. A statistical framework that quantifies the probability of each variant to be causal while allowing an arbitrary number of causal variants.'
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.'
CBLAS'C interface to the BLAS'
cclib'cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner. '
cddlib'An efficient implementation of the Double Description Method'
CD-HIT'CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.'
CDO'CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.'
cdsapi'Climate Data Store API'
Centrifuge'Classifier for metagenomic sequences'
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. This module provides the installation dependancies. You must check out CESM from git in your workspace.'
CFITSIO'CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.'
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.'
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.'
CGmapTools'Command-line Toolset for Bisulfite Sequencing Data Analysis'
cgmlst-dists'Calculate distance matrix from cgMLST allele call tables of ChewBBACA'
cgMLSTFinder'Core genome Multi-Locus Sequence Typing'
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.'
charmm'CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm (CHARMM lite) provides all the functionality of CHARMM except its performance enhancements.'
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.'
CheckM'CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.'
Cheetah'Cheetah is an open source template engine and code generation tool.'
CheMPS2'CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.'
chewBBACA'chewBBACA stands for "BSR-Based Allele Calling Algorithm". chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.'
ChimPipe'ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution.'
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.'
CITE-seq-Count'A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.'
Clang'C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.'
Clang-Python-bindings'Python bindings for libclang'
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.'
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.'
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. '
CNVkit'A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.'
CoCoALib'CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra.'
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.'
Comsol''
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.'
CoordgenLibs'Schrodinger-developed 2D Coordinate Generation'
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. '
corner'Make some beautiful corner plots.'
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. '
cram'Cram is a functional testing framework for command line applications.'
crb-blast'Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.'
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. '
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.'
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.'
ctffind'Program for finding CTFs of electron micrographs.'
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. '
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. '
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. '
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.'
CUDAcore'CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.'
cuDNN'The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.'
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. '
cutadapt'Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.'
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. '
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. '
Cython'Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). '
cytosim'Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).'
cyvcf2'cython + htslib == fast VCF and BCF processing'
DANPOS3'A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2'
dask'Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.'
DB'Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.'
DBD-mysql'Perl binding for MySQL'
DB_File'Perl5 access to Berkeley DB version 1.x.'
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. '
dbus-glib'D-Bus is a message bus system, a simple way for applications to talk to one another.'
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.'
deepdiff'DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.'
DeepSurv'DeepSurv is a deep learning approach to survival analysis. '
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.'
DendroPy'A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.'
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.'
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.'
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. '
DIAMOND'Accelerated BLAST compatible local sequence aligner'
DIRAC'DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations'
DL_POLY_Classic'DL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package.'
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.'
dm-tree'dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.'
double-conversion'Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.'
DoubletFinder'R package for detecting doublets in single-cell RNA sequencing data'
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. '
dtcmp'Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI. '
dtcwt'Dual-Tree Complex Wavelet Transform library for Python'
E-ANTIC'E-ANTIC is a C/C++ library to deal with real embedded number fields built on top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as possible exact arithmetic operations and comparisons.'
EasyBuild'EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.'
EasyBuild-grace'EasyBuild environment variables for building system software in /tmp and installing in /sw/eb on grace.hprc.tamu.edu'
EasyBuild-grace-myeb'User EasyBuild environment for grace.hprc.tamu.edu in $SCRATCH/eb'
EasyBuild-grace-SCRATCH'User EasyBuild environment for grace.hprc.tamu.edu in $SCRATCH/eb'
EasyBuild-grace-tmp'EasyBuild environment variables for building in /tmp and installing in /sw/eb on grace.hprc.tamu.edu'
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).'
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).'
edlib'Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.'
Eigen'Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.'
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.'
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. '
ELPA'Eigenvalue SoLvers for Petaflop-Applications .'
ELPH'ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). '
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. '
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.'
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! '
EMU'EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets '
EnsEMBLCoreAPI'The Ensembl Core Perl API and SQL schema'
ESMF'The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.'
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. '
Essentia'Open-source library and tools for audio and music analysis, description and synthesis'
ETE'A Python framework for the analysis and visualization of trees'
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. '
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) '
FabIO'FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats).'
FALCON'Falcon: a set of tools for fast aligning long reads for consensus and assembly'
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.'
FastME'FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.'
fastp'A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.'
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.'
FastQ_Screen'FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.'
FastQTL'FastQTL is a QTL mapper'
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'
fastsimcoal26'fast sequential Markov coalescent simulation of genomic data under complex evolutionary models'
fastStructure'fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. '
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. '
FastViromeExplorer'Identify the viruses/phages and their abundance in the viral metagenomics data.'
FDS'Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.'
FEMZIP-L'FEMZIP-L is a data compression software package for LS-DYNA result files - Homepage: http://www.sidact.com/femzip-crash.html '
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.'
festival'University of Edinburgh's Festival Speech Synthesis Systems is a free software multi-lingual speech synthesis workbench that runs on multiple-platforms offering black box text to speech, as well as an open architecture for research in speech synthesis. It designed as a component of large speech technology systems. '
fetchMG'The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes in an easy and accurate manner.'
FFmpeg'A complete, cross-platform solution to record, convert and stream audio and video.'
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.'
FigureGen'FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps. '
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.'
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.'
Firefox'Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.'
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. '
flatbuffers'FlatBuffers: Memory Efficient Serialization Library'
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. '
Flexbar'The program Flexbar preprocesses high-throughput sequencing data efficiently'
FlexiDot'Highly customizable, ambiguity-aware dotplots for visual sequence analyses '
FLINT'FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.'
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.'
Flye'Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.'
FMILibrary'FMI library is intended as a foundation for applications interfacing FMUs (Functional Mockup Units) that follow FMI Standard. This version of the library supports FMI 1.0 and FMI2.0. See http://www.fmi-standard.org/'
fontconfig'Fontconfig is a library designed to provide system-wide font configuration, customization and application access. '
foss'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
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.'
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.'
FreeSurfer'FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.'
freetype'FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. '
FreeXL'FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. '
FriBidi'The Free Implementation of the Unicode Bidirectional Algorithm. '
FSL'FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.'
FTGL'FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. '
FuSeq'FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data.'
future'python-future is the missing compatibility layer between Python 2 and Python 3.'
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'
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.'
gams'The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. It consists of a language compiler and a stable of integrated high-performance solvers. GAMS is tailored for complex, large scale modeling applications, and allows you to build large maintainable models that can be adapted quickly to new situations. traditional programming languages such as C, C++, and Fortran.'
gap'GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.'
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.'
GATE'GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography'
GATK'The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.'
Gaussian'Gaussian 16 is the latest version of the Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Gaussian 16 provides a wide-ranging suite of the most advanced modeling capabilities available. You can use it to investigate the real-world chemical problems that interest you, in all of their complexity, even on modest computer hardware. Homepage: http://gaussian.com/ '
gc'The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. '
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,...).'
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,...).'
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.'
Gctf'Gctf: real-time CTF determination and correction, Kai Zhang, 2016'
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.'
gdc-client'The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.'
GDGraph'GDGraph is a Perl package to generate charts'
Gdk-Pixbuf'The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. '
GDRCopy'A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.'
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.'
gearshifft'Benchmark Suite for Heterogenuous FFT Implementations'
GEMMA'Genome-wide Efficient Mixed Model Association'
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. '
GeneMark-ET'Eukaryotic gene prediction suite with automatic training'
GeneMarkS'GeneMarkS - Gene Prediction in Prokaryotes.'
gengetopt'Gengetopt is a tool to write command line option parsing code for C programs.'
GenomeThreader'GenomeThreader is a software tool to compute gene structure predictions.'
GenomeTools'A comprehensive software library for efficient processing of structured genome annotations.'
geocube'Tool to convert geopandas vector data into rasterized xarray data.'
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.'
GEOS'GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)'
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'
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. '
GHC'The Glorious/Glasgow Haskell Compiler'
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.'
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.'
gimkl'GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL'
gimpi'GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.'
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.'
git-lfs'Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com'
GitPython'GitPython is a python library used to interact with Git repositories '
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'
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.'
GLib'GLib is one of the base libraries of the GTK+ project'
GLibmm'C++ bindings for Glib'
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.'
GlobalArrays'Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model'
glog'A C++ implementation of the Google logging module.'
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.'
GMAP-GSNAP'GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program'
GMP'GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. '
gmpy2'GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x'
gmsh'Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.'
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. '
gnuplot'Portable interactive, function plotting utility'
Go'Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.'
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.'
golf'GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW.'
gomkl'GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL'
gompi'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.'
gompic'GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.'
googletest'Google's framework for writing C++ tests on a variety of platforms'
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.'
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. '
gperftools'gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.'
gpustat'dstat-like utilization monitor for NVIDIA GPUs'
Grace'Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.'
gradunwarp'Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.'
GraphicsMagick'GraphicsMagick is the swiss army knife of image processing.'
graphite2'Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.'
GraphMap2'A highly sensitive and accurate mapper for long, error-prone reads'
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.'
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.'
GRASP'The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms.'
gretl'A cross-platform software package for econometric analysis'
groff'Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.'
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. '
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.'
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.'
GTDB-Tk'A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.'
GTK+'The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. '
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. '
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.'
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.'
gzip'gzip (GNU zip) is a popular data compression program as a replacement for compress'
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.'
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.'
Hadoop'Hadoop MapReduce by Cloudera'
HarfBuzz'HarfBuzz is an OpenType text shaping engine.'
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.'
harmony'Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets.'
HDDM'HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC).'
HDF'HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. '
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.'
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.'
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.'
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.'
HeFFTe'Highly Efficient FFT for Exascale (HeFFTe) library'
help2man'help2man produces simple manual pages from the '--help' and '--version' output of other commands.'
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.'
hierfstat'Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy.'
hifiasm'Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads. It can assemble a human genome in several hours and assemble a ~30Gb California redwood genome in a few days. Hifiasm emits partially phased assemblies of quality competitive with the best assemblers. Given parental short reads or Hi-C data, it produces arguably the best haplotype-resolved assemblies so far. '
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).'
HLAminer'HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads. '
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.'
HMMER2'HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.'
Horovod'Horovod is a distributed training framework for TensorFlow.'
horton'HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost. Although HORTON is primarily designed to be a quantum-chemistry program, it can perform computations involving model Hamiltonians, and could be extended for computations in nuclear physics.'
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.'
htop'Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. '
HTSeq'HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.'
HTSlib'A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix'
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. '
hyperopt'Distributed Asynchronous Hyperparameter Optimization in Python'
Hyperopt'hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions.'
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'
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.'
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.'
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'
iccifort'Intel C, C++ & Fortran compilers'
iccifortcuda'Intel C, C++ & Fortran compilers with CUDA toolkit'
ichorCNA'ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing'
iCount'iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.'
ICU'ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.'
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.'
ifort'Intel Fortran compiler'
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++.'
IGV'This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.'
igv-reports'Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.'
iimpi'Intel C/C++ and Fortran compilers, alongside Intel MPI.'
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. '
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.'
ImageMagick'ImageMagick is a software suite to create, edit, compose, or convert bitmap images'
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'
imbalanced-learn'imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.'
imgaug'This python library helps you with augmenting images for your machine learning projects. It converts a set of input images into a new, much larger set of slightly altered images. '
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.'
immunedeconv'immunedeconv is an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.'
impi'Intel MPI Library, compatible with MPICH ABI'
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.'
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).'
intelcuda'Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit'
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. '
intltool'intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.'
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.'
iomkl'Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.'
iompi'Intel C/C++ and Fortran compilers, alongside Open MPI.'
IOR'The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. '
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. '
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.'
IQ-TREE'Efficient phylogenomic software by maximum likelihood'
IRkernel'The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.'
ITK'Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.'
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.'
ITSTool'ITS Tool allows you to translate your XML documents with PO files, using rules from the W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages.'
iVar'iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. '
JAGS'JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation '
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. '
Java'Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.'
JavaCyc'Javacyc is a java class for accessing internal Pathway-Tools functions.'
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.'
JCVI'Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.'
Jellyfish'Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.'
jemalloc'jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.'
JiTCODE'Just-in-time compilation for ordinary/delay/stochastic differential equations (DDEs)'
joypy'Joyplots in Python with matplotlib & pandas'
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. '
Judy'A C library that implements a dynamic array.'
Julia'Julia is a high-level, high-performance dynamic programming language for numerical computing'
JUnit'A programmer-oriented testing framework for Java.'
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.'
Kaiju'Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments'
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.'
KAT'The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.'
kedro'Kedro is an open-source Python framework that applies software engineering best-practice to data and machine-learning pipelines. '
Kent_tools'Kent utilities: collection of tools used by the UCSC genome browser.'
Keras'Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.'
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. '
kma'KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.'
KMC'KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.'
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.'
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.'
KronaTools'Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.'
kwant'Kwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport.'
KyotoCabinet'Kyoto Cabinet is a library of routines for managing a database.'
LAME'LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.'
LAMMPS'LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. Includes support for On-the-fly Calculation of Transport Properties (OCTP), see https://github.com/omoultosEthTuDelft/OCTP '
LAST'LAST finds similar regions between sequences.'
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. '
lavaan'lavaan is a free, open source R package for latent variable analysis'
leidenalg'Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.'
LevelDB'LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.'
libaio'Asynchronous input/output library that uses the kernels native interface.'
libarchive'Multi-format archive and compression library '
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. '
libcircle'An API to provide an efficient distributed queue on a cluster. libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization. '
libcroco'Libcroco is a standalone css2 parsing and manipulation library.'
libdap'A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes.'
libdrm'Direct Rendering Manager runtime library.'
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))'
libelf'libelf is a free ELF object file access library'
libepoxy'Epoxy is a library for handling OpenGL function pointer management for you'
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. '
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. '
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. '
libFLAME'libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK.'
libgcrypt'Libgpg-error is a small library that defines common error values for all GnuPG components.'
libgd'GD is an open source code library for the dynamic creation of images by programmers.'
libgeotiff'Library for reading and writing coordinate system information from/to GeoTIFF files'
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. '
libglvnd'libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.'
libgpg-error'Libgpg-error is a small library that defines common error values for all GnuPG components.'
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.'
libharu'libHaru is a free, cross platform, open source library for generating PDF files.'
libiconv'Libiconv converts from one character encoding to another through Unicode conversion'
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.'
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.'
LiBis'An ultrasensitive alignment method for low input bisulfite sequencing'
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. '
libmatheval'GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.'
libobjcryst'ObjCryst++ is Object-Oriented Crystallographic Library for C++'
libosmium'A fast and flexible C++ library for working with OpenStreetMap data. The Osmium Library has extensive support for all types of OSM entities: nodes, ways, relations, and changesets. It allows reading from and writing to OSM files in XML and PBF formats, including change files and full history files. Osmium can store OSM data in memory and on disk in various formats and using various indexes. Its easy to use handler interface allows you to quickly write data filtering and conversion functions. Osmium can create WKT, WKB, OGR, GEOS and GeoJSON geometries for easy conversion into many GIS formats and it can assemble multipolygons from ways and relations.'
libpciaccess'Generic PCI access library.'
libpng'libpng is the official PNG reference library'
libpsl'C library for the Public Suffix List'
libPSML'A library to handle PSML, the pseudopotential markup language.'
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. '
libRmath'The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.'
librsvg'librsvg is a library to render SVG files using cairo.'
libsamplerate'Secret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio.'
libsigc++'The libsigc++ package implements a typesafe callback system for standard C++.'
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.'
libsodium'Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. '
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.'
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.'
LibTIFF'tiff: Library and tools for reading and writing TIFF data files'
libtirpc'Libtirpc is a port of Suns Transport-Independent RPC library to Linux.'
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. '
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'
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.'
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.'
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.'
libxml++'libxml++ is a C++ wrapper for the libxml XML parser library.'
libxml2'Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). '
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.'
libxslt'Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).'
libxsmm'LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).'
libyaml'LibYAML is a YAML parser and emitter written in C.'
libzeep'Libzeep was originally developed to make it easy to create SOAP servers.'
lifelines'lifelines is a pure Python implementation of the best parts of survival analysis'
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 '
Lighter'Fast and memory-efficient sequencing error corrector'
LittleCMS'Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. '
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.'
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.'
LMfit'Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python'
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.'
Longshot'Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).'
lpsolve'Mixed Integer Linear Programming (MILP) solver'
lrslib'lrslib is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems'
LSD2'Least-squares methods to estimate rates and dates from phylogenies'
LS-DYNA'LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. - Homepage: http://www.lstc.com/products/ls-dyna/ '
LS-OPT'LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA. - Homepage: http://www.lstc.com/products/ls-opt/ '
LS-PREPOST'LS-PREPOST is an advanced pre and post-processor that is delivered free with LS-DYNA. - Homepage: http://www.lstc.com/lspp '
LS-TASC'LS-TaSC is a Topology and Shape Computation tool. Developed for engineering analysts who need to optimize structures. - Homepage: http://www.lstc.com/products/ls-tasc/ '
LtrDetector'A modern tool-suite for detectinglong terminal repeat retrotransposons de-novo onthe genomic scale'
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.'
LUSCUS'Luscus is the program for graphical display and editing of molecular systems.'
lwgrp'The Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups '
lxml'The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.'
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.'
LZO'Portable lossless data compression library'
M4'GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. '
MACS2'Model Based Analysis for ChIP-Seq data'
maeparser'maeparser is a parser for Schrodinger Maestro 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.'
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.'
MAGMA'MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.'
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. '
make'GNU version of make utility'
makedepend'The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.'
makeinfo'makeinfo is part of the Texinfo project, the official documentation format of the GNU project.'
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.'
Mako'A super-fast templating language that borrows the best ideas from the existing templating languages'
manta'Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. '
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.'
MariaDB-connector-c'MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.'
Mash'Fast genome and metagenome distance estimation using MinHash'
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).'
MATIO'matio is an C library for reading and writing Matlab MAT files.'
Matlab'A numerical computing environment and fourth-generation programming language. - Homepage: http://www.mathworks.com/products/matlab/ '
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.'
Mauve'Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.'
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. '
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.'
MBROLA'https://github.com/numediart/MBROLA-voices'] 'MBROLA is a speech synthesizer based on the concatenation of diphones. It takes a list of phonemes as input, together with prosodic information (duration of phonemes and a piecewise linear description of pitch), and produces speech samples on 16 bits (linear), at the sampling frequency of the diphone database. MBROLA voices project provides list of MBROLA speech synthesizer voices. It is intended to provide easier collaboration and automatic updates for individual users and packagers. '
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. '
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.'
MDSplus'MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.'
MDSplus-Python'MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.'
MDTraj'Read, write and analyze MD trajectories with only a few lines of Python code.'
medaka'medaka is a tool to create a consensus sequence from nanopore sequencing data.'
medImgProc'Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation.'
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.'
MEGAHIT'An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph'
MEM'Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores.'
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.'
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.'
Mesa'Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.'
meshalyzer'Graphical program for display time dependent data on 3D finite elment meshes'
meshtool'Meshtool is a comand-line tool written in C++. It is designed to apply various manipulations to volumetric meshes.'
Meson'Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.'
Mesquite'Mesh-Quality Improvement Library'
MESS'Master Equation System Solver (MESS)'
MetaBAT'An efficient tool for accurately reconstructing single genomes from complex microbial communities'
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.'
metaerg'MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline.'
MetaEuk'MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.'
MetaPhlAn2'MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.'
Metassembler'Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies.'
metaWRAP'MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.'
Metaxa2'Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically'
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. '
MinCED'Mining CRISPRs in Environmental Datasets'
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.'
Mini-XML'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.'
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.'
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).'
miRDeep2'miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs '
misha'The misha package is intended to help users to efficiently analyze genomic data achieved from various experiments.'
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.'
mkl-dnn'Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)'
mkl_fft'NumPy-based Python interface to Intel(R) MKL FFT functionality'
mlst'Scan contig files against traditional PubMLST typing schemes'
MLST_Check'Multilocus sequence typing by blast using the schemes from PubMLST.'
MLxtend'Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks.'
MMseqs2'MMseqs2: ultra fast and sensitive search and clustering suite'
MOABS'MOABS: MOdel based Analysis of Bisulfite Sequencing data'
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.'
Mono'An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.'
Monocle3'An analysis toolkit for single-cell RNA-seq. '
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.'
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.'
MotionCor2'MotionCor2 correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 '
motionSegmentation'Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation.'
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.'
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.'
MPFR'The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. '
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.'
mpifileutils'MPI-Based File Utilities For Distributed Systems '
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. '
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.'
MRChem'MRChem is a numerical real-space code for molecular electronic structure calculations within the self-consistent field (SCF) approximations of quantum chemistry: Hartree-Fock and Density Functional Theory.'
MRCPP'MultiResolution Computation Program Package'
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.'
msprime'msprime is a coalescent simulator and library for processing tree-based genetic data.'
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.'
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.'
MUMmer'MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.'
MUMPS'A parallel sparse direct solver. This module is for its sequential variant.'
MuPeXI'MuPeXI: Mutant Peptide eXtractor and Informer. Given a list of somatic mutations (VCF file) as input, MuPeXI returns a table containing all mutated peptides (neo-peptides) of user-defined lengths, along with several pieces of information relevant for identifying which of these neo-peptides are likely to serve as neo-epitopes.'
MUSCLE'MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.'
MUST'MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers that want to develop correct MPI applications. This includes errors that already manifest – segmentation faults or incorrect results – as well as many errors that are not visible to the application developer or do not manifest on a certain system or MPI implementation.'
NAMD'NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.'
NanoComp'Comparing runs of Oxford Nanopore sequencing data and alignments'
nanocompore'Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples'
nanofilt'Filtering and trimming of long read sequencing data.'
NanoFilt'Filtering and trimming of Oxford Nanopore Sequencing data'
nanoget'Functions to extract information from Oxford Nanopore sequencing data and alignments'
nanomath'A few simple math function for other Oxford Nanopore processing scripts'
NanoPlot'Plotting suite for long read sequencing data and alignments'
nanopolish'Software package for signal-level analysis of Oxford Nanopore sequencing data.'
NASM'NASM: General-purpose x86 assembler'
nauty'nauty and Traces are programs for computing automorphism groups of graphs and digraphs. They can also produce a canonical label.'
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.'
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'
ncl'The NEXUS Class Library is a C++ library for parsing NEXUS files.'
NCL'NCL is an interpreted language designed specifically for scientific data analysis and visualization.'
NCO'manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5'
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. '
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.'
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. '
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.'
netcdf4-python'Python/numpy interface to netCDF.'
netCDF-C++4'NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.'
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.'
netMHCpan'The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs). '
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.'
networkx'NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.'
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.'
nglview'IPython widget to interactively view molecular structures and trajectories.'
NGS'NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.'
ngspice'Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. '
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.'
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.'
Nilearn'Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.'
Nim'Nim is a systems and applications programming language.'
Ninja'Ninja is a small build system with a focus on speed.'
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.'
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.'
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. '
NLTK'NLTK is a leading platform for building Python programs to work with human language data.'
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.'
Normaliz'Normaliz is an open source tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones.'
NSPR'Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.'
NSS'Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.'
nsync'nsync is a C library that exports various synchronization primitives, such as mutexes'
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. '
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.'
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.'
NVBIO'NVBIO is a library of reusable components designed by NVIDIA Corporation to accelerate bioinformatics applications using CUDA. It contains the nvBowtie and nvLighter applications.'
nvtop'htop-like GPU usage monitor'
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.'
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.'
OCNet'Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology.'
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. '
OpenAI-Gym'A toolkit for developing and comparing reinforcement learning algorithms.'
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.'
OpenBLAS'OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.'
openCARP'openCARP is an open cardiac electrophysiology simulator for in-silico experiments.'
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.'
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.'
Open-Data-Cube-Core'The Open Data Cube Core provides an integrated gridded data analysis environment for decades of analysis ready earth observation satellite and related data from multiple satellite and other acquisition systems.'
OpenEXR'OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications'
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.'
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.'
OpenForceField'Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.'
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.'
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.'
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. '
OpenMM'OpenMM is a toolkit for molecular simulation.'
OpenMMTools'A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages. '
OpenMolcas'OpenMolcas is a quantum chemistry software package'
OpenMPI'The Open MPI Project is an open source MPI-3 implementation.'
OpenPGM'OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. '
OpenPIV'OpenPIV is an open source Particle Image Velocimetry analysis software'
OpenSees'Open System for Earthquake Engineering Simulation'
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. '
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.'
OptiType'OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. '
orca'Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line.'
ORCA'ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. '
OrthoFinder'OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics'
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.'
OSU-Micro-Benchmarks'OSU Micro-Benchmarks'
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. '
p4vasp'Visualization suite for VASP'
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.'
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.'
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. '
parallel'parallel: Build and execute shell commands in parallel'
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. '
ParaView'ParaView is a scientific parallel visualizer.'
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.'
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.'
PartitionFinder'PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks.'
PAUP'PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees.'
pauvre'Tools for plotting Oxford Nanopore and other long-read data'
pbbam'The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices.'
pbcopper'The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications.'
pbmm2'A minimap2 frontend for PacBio native data formats'
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. '
PCRE2'The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. '
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. '
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.'
Percolator'Semi-supervised learning for peptide identification from shotgun proteomics datasets'
Perl'Larry Wall's Practical Extraction and Report Language'
PerlCyc'Perlcyc.pm is a Perl module for accessing internal Pathway-Tools functions.'
PEST++'PEST++ is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model. '
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. '
pFUnit'pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran.'
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.'
pHierCC'HierCC is a multi-level clustering scheme for population assignments based on core genome Multi-Locus Sequence Types (cgMLSTs).'
Phobius'Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.'
phonemizer'The phonemizer allows simple phonemization of words and texts in many languages. Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. It is using four backends: espeak, espeak-mbrola, festival and segments. '
phonopy'Phonopy is an open source package of phonon calculations based on the supercell approach.'
phylokit'C++ library for high performance phylogenetics'
phylonaut'Dynamic programming for phylogenetics applications'
PhyML'Phylogenetic estimation using (Maximum) Likelihood'
phyx'phyx performs phylogenetics analyses on trees and sequences.'
picard'A set of tools (in Java) for working with next generation sequencing data in the BAM format.'
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. '
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.'
Pillow-SIMD'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.'
Pilon'Pilon is an automated genome assembly improvement and variant detection tool'
Pingouin'Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy.'
Pint'Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units.'
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.'
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. '
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'
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). '
PlantClusterFinder'A pipeline to predict metabolic gene clusters from plant genomes'
plantcv'PlantCV: Plant phenotyping using computer vision.'
PlaScope'Plasmid exploration of bacterial genomes'
PlasFlow'PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.'
PlasmaPy'Open source Python ecosystem for plasma research and education'
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). '
PLINK'PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).'
plotly.py'An open-source, interactive graphing library for Python'
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. '
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. '
PnetCDF'Parallel netCDF: A Parallel I/O Library for NetCDF File Access'
pocl'Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard'
poetry'Python packaging and dependency management made easy'
poppler'Poppler is a PDF rendering library based on the xpdf-3.0 code base.'
popscle'A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools '
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'
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.'
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.'
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.'
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).'
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.'
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.'
PROJ'Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates'
ProjectQ'An open source software framework for quantum computing'
prokka'Prokka is a software tool for the rapid annotation of prokaryotic genomes.'
protobuf'Google Protocol Buffers'
protobuf-python'Python Protocol Buffers runtime library.'
protozero'Minimalistic protocol buffer decoder and encoder in C++.'
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.'
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.'
psutil'A cross-platform process and system utilities module for Python'
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.'
pullseq'Utility program for extracting sequences from a fasta/fastq file'
pybedtools'pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.'
PyBerny'PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information.'
pyBigWig'A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.'
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.'
PyCairo'Python bindings for the cairo library'
pycocotools'Official APIs for the MS-COCO dataset'
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.'
PyCUDA'PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.'
PycURL'PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features.'
pydantic'Data validation and settings management using Python type hinting.'
pydot'Python interface to Graphviz's Dot language.'
pyFFTW'A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms.'
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)'
PyFR'PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine.'
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.'
PyGObject'Python Bindings for GLib/GObject/GIO/GTK+'
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.'
pygrib'Python interface for reading and writing GRIB data'
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'
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).'
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.'
PyMC3'Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano'
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.'
pyobjcryst'Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library.'
Pyomo'Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. '
PyOpenCL'PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.'
PyOpenGL'PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.'
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.'
pyproj'Python interface to PROJ4 library for cartographic transformations'
pyqstem'QSTEM is a program for quantitative image simulation in electron microscopy, including TEM, STEM and CBED image simulation. This project interfaces the QSTEM code with Python and the Atomic Simulation Environment (ASE) to provide a single environment for building models, simulating and analysing images.'
PyQt5'PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.'
PyQtGraph'PyQtGraph is a pure-python graphics and GUI library built on PyQt4/PySide and numpy.'
PyRe'PyRe (Python Reliability) is a Python module for structural reliability analysis.'
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.'
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.'
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.'
PySCF'PySCF is an open-source collection of electronic structure modules powered by Python.'
pysndfx'A lightweight Python wrapper for SoX - Sound eXchange. Supported effects range from EQ and compression to phasers, reverb and pitch shifters.'
Pysolar'Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun.'
pyspoa'Python bindings to spoa.'
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.'
pytest'pytest: simple powerful testing with Python'
Python'Python is a programming language that lets you work more quickly and integrate your systems more effectively.'
python-igraph'Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.'
python-Levenshtein'Python extension for computing string edit distances and similarities.'
python-parasail'Python Bindings for the Parasail C Library'
python-weka-wrapper3'Python3 wrapper for the Weka Machine Learning Workbench'
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. '
PyTorch'Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.'
PyTorch-Geometric'PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.'
PyVCF'A Variant Call Format reader for Python.'
PyWavelets'PyWavelets is open source wavelet transform software for Python.'
PyYAML'PyYAML is a YAML parser and emitter for the Python programming language.'
PyZMQ'Python bindings for ZeroMQ'
Q6'EVB, FEP and LIE simulator.'
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'
qchem'Q-Chem 5.4.0 release environment module'
qcint'libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform.'
QDD'A user-friendly program to select microsatellite markers and design primers from large sequencing projects.'
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. '
Qiskit'Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms.'
qpth'A fast and differentiable QP solver for PyTorch. '
qrupdate'qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.'
Qt'Qt is a comprehensive cross-platform C++ application framework.'
Qt5'Qt is a comprehensive cross-platform C++ application framework.'
Qt5Webkit'Qt Port of WebKit. WebKit is an open source web browser engine.'
Qualimap'Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.'
Quandl'A Python library for Quandl’s RESTful API.'
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). '
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.'
QuickFF'QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations.'
quickmerge'The program uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore.'
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.'
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.'
Racon'Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.'
rainbow'Efficient tool for clustering and assembling short reads, especially for RAD.'
rampart'Read Assignment, Mapping, and Phylogenetic Analysis in Real Time.'
randfold'Minimum free energy of folding randomization test software'
RapidJSON'A fast JSON parser/generator for C++ with both SAX/DOM style API'
raspa'The The RASPA software is a general purpose classical simulation package especially suited to study adsorption and diffusion in nanoporous systems. The iRASPA package is an advanced visualization package. We regularly organize workshops and school to teach students advanced, state-of-the-art molecular simulation techniques through practical use (in addition to theory).'
rasterio'Rasterio reads and writes geospatial raster data.'
rasterstats'rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries.'
RAxML'RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.'
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.'
Ray-project'Ray is a fast and simple framework for building and running distributed applications.'
RBFOpt'RBFOpt is a Python library for black-box optimization (also known as derivative-free optimization).'
R-bundle-Bioconductor'Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.'
RDFlib'RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.'
RDKit'RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.'
RE2'RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library. '
re2c're2c 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.'
Reapr'A tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison.'
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'
RepeatMasker'RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.'
rgdal'Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library.'
rgeos'R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries'
rickflow'Running and Analyzing OpenMM Jobs'
rioxarray'geospatial xarray extension powered by rasterio'
rjags'The rjags package is an interface to the JAGS library.'
R-keras'Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. '
rMATS-turbo'rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net).'
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.'
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.'
RNAIndel'RNAIndel calls coding indels and classifies them into somatic, germline, and artifact from tumor RNA-Seq data.'
rnaQUAST'rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.'
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.'
RNAz'RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.'
RnBeads'RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution.'
Roary'Rapid large-scale prokaryote pan genome analysis'
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.'
rpy2'rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions. '
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.'
rstanarm'Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation.'
R_tamu''
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. '
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.'
Rust'Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.'
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. '
SalmID'Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).'
Salmon'Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.'
SALMON-TDDFT'SALMON is an open-source computer program for ab-initio quantum-mechanical calculations of electron dynamics at the nanoscale that takes place in various situations of light-matter interactions. It is based on time-dependent density functional theory, solving time-dependent Kohn-Sham equation in real time and real space with norm-conserving pseudopotentials.'
SALSA'A tool to scaffold long read assemblies with Hi-C'
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.'
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.'
ScaFaCoS'ScaFaCoS is a library of scalable fast coulomb solvers.'
ScaLAPACK'The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.'
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. '
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.'
scikit-bio'scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.'
scikit-build'Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.'
scikit-image'scikit-image is a collection of algorithms for image processing.'
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.'
scikit-optimize'Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions.'
scikit-uplift'scikit-uplift is a Python module for classic approaches for uplift modeling built on top of scikit-learn. Uplift prediction aims to estimate the causal impact of a treatment at the individual level. '
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.'
SciPy-bundle'Bundle of Python packages for scientific software'
SCons'SCons is a software construction tool.'
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. '
SCOTCH'Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.'
scp'The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol.'
scVelo'scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling.'
SDL2'SDL: Simple DirectMedia Layer, a cross-platform multimedia library'
Seaborn'Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. '
SECAPR'SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments'
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. '
segmentation-models'Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow.'
SentencePiece'Unsupervised text tokenizer for Neural Network-based text generation.'
sep'Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only)'
SEPP'SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.'
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'SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation'
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.'
SeqSero2'Salmonella serotyping from genome sequencing data. SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. '
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'
Seurat'Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.'
sf'Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations.'
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.'
shapAAR'An R package for the extraction, analysis and classification of (not only) archaeological objects from scanned images.'
SHAPEIT4'SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. '
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.'
Short-Pair'Sensitive Short Read Homology Search for Paired-End Reads'
shovill'Faster SPAdes assembly of Illumina reads'
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.'
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. '
SimPEG'Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.'
SimpleElastix'Multi-lingual medical image registration library.'
SimpleITK'imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.'
simpy'SimPy is a process-based discrete-event simulation framework based on standard Python.'
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. '
SIP'SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.'
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.'
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.'
SMARTdenovo'SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.'
SMRT-Link'PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided'
snakemake'The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.'
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.'
Snoscan'Search for C/D box methylation guide snoRNA genes in a genomic sequence. '
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. '
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.'
SPAdes'Genome assembler for single-cell and isolates data sets'
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.'
Spark'Spark is Hadoop MapReduce done in memory'
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. '
spatialreg'A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep', 'sphet' and 'spse'.'
speech_tools'The Edinburgh Speech Tools Library is a collection of C++ class, functions and related programs for manipulating the sorts of objects used in speech processing. It includes support for reading and writing waveforms, parameter files (LPC, Ceptra, F0) in various formats and converting between them. It also includes support for linguistic type objects and support for various label files and ngrams (with smoothing). '
spglib-python'Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.'
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.'
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.'
SPLASH'SPLASH is a free and open source visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations.'
spoa'Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences'
Spyder'Spyder is an interactive Python development environment providing MATLAB-like features in a simple and light-weighted software.'
SQLite'SQLite: SQL Database Engine in a C Library'
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'
SRPRISM'Single Read Paired Read Indel Substitution Minimizer'
SSN'Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.'
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. '
Staden'A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.'
STAR'STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.'
STAR-CCM+'Software for solving problems involving flow (of fluids or solids), heat transfer and stress. - Homepage: http://www.cd-adapco.com/products/star-ccm '
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.'
stars'Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in R, using GDAL bindings provided by sf, and NetCDF bindings by ncmeta and RNetCDF.'
Statistics-R'Perl interface with the R statistical program'
statsmodels'Statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration.'
STEAK'Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS data. The software performs on both single-end (SE) and paired-end ( PE) libraries and on a variety of HTS sequencing strategies. It can be applied to a broad range of research interests and clinical uses such as population genetic studies and detecting polymorphic integrations.'
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.'
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.'
StringTie'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts'
Structure'The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.'
Structure_threader'A program to parallelize the runs of Structure, fastStructure and MavericK software.'
Subread'High performance read alignment, quantification and mutation discovery'
Subversion'Subversion is an open source version control system.'
SuiteSparse'SuiteSparse is a collection of libraries manipulate sparse matrices.'
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. '
SUNDIALS'SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers'
SunPy'The community-developed, free and open-source solar data analysis environment for Python.'
SuperLU'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.'
SVDquest'SVDquartets-based species trees'
SVG'Perl binding for SVG'
swarm'A robust and fast clustering method for amplicon-based studies '
SWIG'SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.'
swissknife'Perl module for reading and writing UniProtKB data in plain text format.'
SymEngine'SymEngine is a standalone fast C++ symbolic manipulation library.'
SYMPHONY'SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C.'
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.'
Szip'Szip compression software, providing lossless compression of scientific data '
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.'
Taiyaki'Taiyaki is research software for training models for basecalling Oxford Nanopore reads.'
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.'
taxator-tk'A set of programs for the taxonomic analysis of nucleotide sequence data'
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.'
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. '
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.'
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.'
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. '
Telescope'Single locus resolution of Transposable ELEment expression using next-generation sequencing.'
tensorboardX'Tensorboard for PyTorch.'
TensorFlow'An open-source software library for Machine Intelligence'
tensorflow-probability'TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.'
TEtranscripts'TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements. TEtranscripts then performs differential analysis using DESeq2.'
texinfo'Texinfo is the official documentation format of the GNU project.'
Theano'Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.'
Thermo-Calc'Thermocalc is a software package for thermodynamic calculations. It is widely used for a variety of calculations.'
thurstonianIRT'Fit Thurstonian IRT models in R using Stan, lavaan, or Mplus'
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. '
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.'
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.'
TINKER'The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.'
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.'
Tkinter'Tkinter module, built with the Python buildsystem'
TMHMM'Prediction of transmembrane helices in proteins.'
Togl'A Tcl/Tk widget for OpenGL rendering.'
Tombo'Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.'
TopHat'TopHat is a fast splice junction mapper for RNA-Seq reads.'
torchaudio'Data manipulation and transformation for audio signal processing, powered by PyTorch '
torchtext'Data loaders and abstractions for text and NLP'
torchvision'Datasets, Transforms and Models specific to Computer Vision'
tqdm'Instantly make your loops show a smart progress meter.'
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.'
treatSens'Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment.'
TRF'Tandem repeats finder: a program to analyze DNA sequences. Legacy version.'
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'
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.'
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. '
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.'
TRIQS'TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. '
TRIQS-cthyb'TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. cthyb = continuous-time hybridisation-expansion quantum Monte Carlo The TRIQS-based hybridization-expansion solver allows to solve the generic problem of a quantum impurity embedded in a conduction bath for an arbitrary local interaction vertex. The “impurity” can be any set of orbitals, on one or several atoms. '
TRIQS-dft_tools'TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. This TRIQS-based-based application is aimed at ab-initio calculations for correlated materials, combining realistic DFT band-structure calculation with the dynamical mean-field theory. Together with the necessary tools to perform the DMFT self-consistency loop for realistic multi-band problems, the package provides a full-fledged charge self-consistent interface to the Wien2K package. In addition, if Wien2k is not available, it provides a generic interface for one-shot DFT+DMFT calculations, where only the single-particle Hamiltonian in orbital space has to be provided. '
TRIQS-tprf'TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. TPRF is a TRIQS-based two-particle response function tool box that implements basic operations for higher order response functions such as inversion, products, the random phase approximation, the bethe salpeter equation (in the local vertex approximation), etc.. The aim is to provide efficient (C++/OpenMP/MPI) implementations of the basic operations needed to compute the two-particle response in the different two-particle channels (particle-hole, particle-particle). '
tRNAscan-SE'Search for tRNA genes in genomic sequences.'
Trycycler'Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes.'
tsne'Python library containing T-SNE algorithms.'
typing-extensions'Typing Extensions – Backported and Experimental Type Hints for Python'
UCLUST'UCLUST: Extreme high-speed sequence clustering, alignment and database search.'
ucsctest'Tools from the UCSC browser..'
UCSCtools'Tools from the UCSC browser..'
UCX'Unified Communication X An open-source production grade communication framework for data centric and high-performance applications '
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.'
umi4cPackage'umi4cPackage is a processing and analysis pipeline for UMI-4C experiment.'
UMI-tools'Tools for handling Unique Molecular Identifiers in NGS data sets'
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. '
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.'
UQTk'The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions.'
utf8proc'utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.'
util-linux'Set of Linux utilities'
V8'R interface to Google's open source JavaScript engine'
Valgrind'Valgrind: Debugging and profiling tools'
variant_tools'Variant tools is a software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.'
vasp'The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. - Homepage: http://www.vasp.at'
vcflib'vcflib is 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.'
velocyto'Velocyto is a library for the analysis of RNA velocity.'
Velvet'Sequence assembler for very short reads'
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.'
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.'
VirtualGL'VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration.'
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.'
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.'
vt'A tool set for short variant discovery in genetic sequence data.'
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.'
wandb'CLI and Python API for Weights and Biases (wandb), a tool for visualizing and tracking your machine learning experiments.'
Wannier90'A tool for obtaining maximally-localised Wannier functions'
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. '
WebKitGTK+'WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit’s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions.'
WebProxy'WebProxy module sets up web proxy environment variables, http_proxy and https_proxy, for internet acceess from the compute nodes. Wiki page: https://hprc.tamu.edu/wiki/SW:WebProxy '
WebSocket++'WebSocket++ is an open source (BSD license) header only C++ library that implements RFC6455 The WebSocket Protocol. '
wget'GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.'
wheel'A built-package format for Python.'
WisecondorX'WisecondorX -- an evolved WISECONDOR'
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 https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.'
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.'
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.'
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. '
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++.'
wxWidgets'wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.'
X11'The X Window System (X11) is a windowing system for bitmap displays'
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. '
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. '
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.'
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. '
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.'
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.'
XGBoost'XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.'
Xmipp'Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. '
xmlf90'xmlf90 is a basic XML parsing library written in Fortran.'
XML-LibXML'Perl binding for libxml2'
XML-Parser'This is a Perl extension interface to James Clark's XML parser, expat.'
xorg-macros'X.org macros utilities.'
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.'
xproto'X protocol and ancillary headers'
XSD'CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler.'
xtb'xtb - An extended tight-binding semi-empirical program package. '
Xvfb'Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.'
XZ'xz: XZ utilities'
yaff'Yaff stands for 'Yet another force field'. It is a pythonic force-field code.'
yak'Yak is initially developed for two specific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads. '
Yasm'Yasm: Complete rewrite of the NASM assembler with BSD license'
YAXT'Yet Another eXchange Tool'
zarr'Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.'
ZEBULON'Zébulon is the state-of-the-art finite element solver of the Z-set suite. - Homepage: http://www.zset-software.com/products/zebulon/ '
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.'
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'
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.'
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.'