Snippets

Alignment Fraction (AF) between two genomes.

annotate genetic variants detected from diverse genomes .

interpreting and visualizing multidimensional data.

C++ standard library.

from High-Throughput Sequencing data.

GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP

Vectorize & thread code or performance “dies”
Easy workflow + data + tips = faster code faster
Prioritize, Prototype & Predict performance gain
Vectorize & thread code or performance “dies”
Easy workflow + data + tips = faster code faster
Prioritize, Prototype & Predict performance gain

so that AVX2 optimised kernels will be used, even when running on an AMD CPU.

the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

IMPORTANT: This version of Anaconda Python comes with Intel MKL support to speed up certain types of mathematical computations, such as linear algebra or FFT. The module sets

       MKL_NUM_THREADS=1

       to run MKL on a single thread by default, avoiding accidental oversubscription
       of cores. The number of threads can be increased for large problems, please
       refer to the Intel MKL documentation for guidance.

the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

IMPORTANT: This version of Anaconda Python comes with Intel MKL support to speed up certain types of mathematical computations, such as linear algebra or FFT. The module sets

       MKL_NUM_THREADS=1

       to run MKL on a single thread by default, avoiding accidental oversubscription
       of cores. The number of threads can be increased for large problems, please
       refer to the Intel MKL documentation for guidance.

a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.

parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units.

phylogenies and testing evolutionary hypotheses.

efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.

Estimation Functional, a description of which can be found here:

http://dx.doi.org/10.1103/PhysRevB.85.235149

Estimation Functional, a description of which can be found here:

http://dx.doi.org/10.1103/PhysRevB.85.235149

for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

BLAS-like dense linear algebra libraries.

and the BOLT-REML algorithm for variance components analysis

and AUGUSTUS in novel eukaryotic genomes.

relatively short nucleotide sequences against a long reference sequence such as the human genome.

using differences in allele frequencies between populations.

analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

determine cytosine methylation states

into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

sequencing reads to long reference sequences.

species in DNA sequences from a metagenomics sample.

comparing protein or nucleotide sequences.

FITS (Flexible Image Transport System) data format.

and reliable geometric algorithms in the form of a C++ library.

a family of tools designed to build, test and package software.

coverage data in multiple samples and linkage data from paired end reads.

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.

particularly designed for ab-initio molecular dynamics.

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.

single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

single cells, or metagenomes.

relationships between objects or positions.

include C++ standard library -- use libstdc++ from GCC.

program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms

biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

without the overhead traditionally associated with such custom projects.

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.

              from genomic and metagenomic datasets.

              from genomic and metagenomic datasets.

IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

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.

EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.

climate, and related models.

matrices, vectors, numerical solvers, and related algorithms.

The target users of Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels.

Also condatains smetana, carveme and memote .

with an emphasis on smoke and heat transport from fires.

in one or more dimensions, of arbitrary input size, and of both real and complex data.

and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

whole-genome Average Nucleotide Identity (ANI).

format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

used by a program without recompiling or relinking it.

and Oxford Nanopore Technologies.

of data on multiple meshes.

FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

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.

as well as libraries for these languages (libstdc++, libgcj,...).

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.

GSNAP: Genomic Short-read Nucleotide Alignment Program

operating on signed integers, rational numbers, and floating point numbers.

method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

This is a GPU enabled build, containing both MPI and threadMPI binaries.

i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

This is a GPU enabled build, containing both MPI and threadMPI binaries.

programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.

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.

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.

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.

storing and managing data between machines.

extremely large and complex data collections.

(both DNA and RNA) against the general human population (as well as against a single reference genome).

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.

of data from high-throughput sequencing (HTS) experiments.

This package includes the utilities bgzip and tabix

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.

support for software applications.

Sequencing data with Highly Uneven Sequencing Depth.

tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data

for RNA structure and sequence similarities.

different protein signature recognition methods into one resource.

software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.

Java applications on desktops and servers.

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.

This version was compiled from source with USE_INTEL_JITEVENTS=1 to enable profiling with VTune.

format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software.

sequencing reads from metagenomic whole genome sequencing experiments

several Bioinformatics tools as well as from text and XML files.

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.

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.

    with additional tests encoding biological consistency and effect relevance

    with additional tests encoding biological consistency and effect relevance

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.

of a pure in-memory database while retaining the persistence of standard disk-based databases.

matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.

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.

and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

metagenomics assembly via succinct de Bruijn graph

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.

floating-point computations with correct rounding.

whether in complete or draft form. AMOS makes use of it.

sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.

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).

the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.

an Expectation-Maximization algorithm.

a system for rendering interactive 3D graphics.

Note that this build enables CPU-based rendering with OpenSWR and LLVM. The module is intended to be used with visualisation software, such as ParaView, on nodes where no GPU hardware is available.

Both on-screen and off-screen rendering are supported.

a system for rendering interactive 3D graphics.

Note that this build enables CPU-based rendering with OpenSWR and LLVM. The module is intended to be used with visualisation software, such as ParaView, on nodes where no GPU hardware is available.

Both on-screen and off-screen rendering are supported.

metagenomic contigs.

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.

This package includes mimicpy

coupled through the MiMiC framework.

assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome, and mitogenome visualization.

the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries.

binary compatible with Microsoft.NET.

to fill the bioinformatics needs of the microbial ecology community.

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.

communication primitives that are performance optimized for NVIDIA GPUs.

Next Generation Sequencing.

and libc-like functions.

of security-enabled client and server applications.

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.

individuals fall into each of a set of user-defined hybrid categories.

that eases writing computational pipelines with complex data

performance metrics and API debugging via a user interface and command line tool.

application’s algorithm, help you select the largest opportunities to optimize, and tune to scale efficiently across any quantity of CPUs and GPUs

It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.

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.

Scientific Visualization applications. Advanced shading effects such as Ambient Occlusion, shadows, and transparency can be rendered interactively, enabling new insights into data exploration.

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.

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.

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.

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.

read whole-slide images (also known as virtual slides).

analyses of DNA or protein sequences using maximum likelihood.

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.

the same syntax and semantics as Perl 5.

and semantics as Perl 5.

scalable (parallel) solution of scientific applications modeled by partial differential equations.

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). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

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.

geographic longitude and latitude coordinates into cartesian coordinates

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.

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.

This version supports CPU-only rendering without X context using the OSMesa library, it does not support GPU rendering.

Use the GALLIUM_DRIVER environment variable to choose a software renderer, it is recommended to use

GALLIUM_DRIVER=swr

for best performance.

Ray tracing using the OSPRay library is also supported.

This version supports CPU-only rendering without X context using the OSMesa library, it does not support GPU rendering.

Use the GALLIUM_DRIVER environment variable to choose a software renderer, it is recommended to use

GALLIUM_DRIVER=swr

for best performance.

Ray tracing using the OSPRay library is also supported.

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

is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.

stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.

This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.

PyTorch is a deep learning framework that puts Python first.

packages for geospatial data I/O, mostly based on the OSGEO libraries GDAL and OGR

from raw DNA sequencing data.

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).

on GEOS and/or GDAL.

of high-throughput genomic data.

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.

assignments from domain to genus, with confidence estimates for each assignment.

            expression engines like those used in PCRE, Perl, and Python. It is a C++library.

            expression engines like those used in PCRE, Perl, and Python. It is a C++library.

in the RFdiffusion paper.

Support for custom matrices ( without KA-Statistics ). Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. Support for cross_match-like masklevel filtering..

needed to handle and analyze large amounts of data in a very efficient way.

needed to handle and analyze large amounts of data in a very efficient way.

collection of tools for processing remote sensing and GIS datasets. The tools are accessed using Python bindings or an XML interface.

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).

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).

For licensing reasons RepBase is not included, instead you must set LIBDIR to point at a directory which contains your copy of it.

multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.

a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.

and guarantees thread safety.

family, pedigree and individual data.

SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format

static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.

for SNP array and high coverage sequencing data.

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.

Real-Time (SMRT) Sequencing data.

NanoMethPhase - Phase long reads and CpG methylations from Oxford Nanopore Technologies.

reads onto genomic reference sequences.

and includes various methods to reformat or summarize SVs.

a variety of high-level programming languages.

transcript-level quantification estimates from RNA-seq data.

redesigned for distributed memory MIMD parallel computers.

for the analysis of sequences with the focus on biological data.

analysis of sequences with the focus on biological data.

microorganisms adapt in different environments.

structure calculations and ab initio molecular dynamics simulations of molecules and solids.

in amino acid sequences from different organisms

from a set of source environments.

software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.

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.

population structure.

that are made from a single whole-genome library from an individual DNA source

to both genes & transposable elements.

genes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes.

suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.

building a graphical user interface (GUI) in many different programming languages.

set of populations.

as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files

paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

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.

analysis of sequences with the focus on biological data.

abilities.

peak performance for 3D and video workloads.

communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.

An open-source production grade communication framework for data centric and high-performance applications

arithmetic manipulation of units, and conversion of values between compatible scales of measurement.

often orders of magnitude faster than BLAST.

where it functions as a SPAdes-optimiser.

materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

Variant Call Format (VCF) files.

methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.

variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.

systems using 3-D graphics and built-in scripting.

Performs chimera detection, clustering, full-length and prefix dereplication, rereplication, 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.

Assembly and Java.

stand-alone programs for the prediction and comparison of RNA secondary structures.

of the de-facto Unix editor 'Vi', with a more complete feature set.

into superior minimizer sampling techniques.

This allows applications that 'require' a GUI to run in a command line environment. Can be invoked with xvfb-run.

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.

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.

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

build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.

metabolite biosynthesis gene clusters in bacterial and fungal genomes.

command line options with a minimum of fuss.

that perform operations on SAM/BAM files.

Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

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.

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.

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

items to be quickly and easily located by a text editor or other utility.

deep neural networks.

deep neural networks.

from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

comparison operations to compare the values of two items which can be arbitrary MPI datatypes.

for preprocessing raw data and building your own custom reference database.

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).

using precomputed eggNOG-based orthology assignments

such as publication, sequence, structure, gene, variation, expression, etc.

in which an application registers handlers for things the parser might find in the XML document (like start tags)

uncommon tasks with FASTQ files.

sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

customization and application access.

OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

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.

scalable, and high performance remote function execution. Unlike centralized FaaS platforms, funcX allows users to execute functions on heterogeneous remote computers, from laptops to campus clusters, clouds, and supercomputers. A funcX endpoint is a persistent service launched by the user on a compute system to serve as a conduit for executing functions on that computer.

Structured Genome Annotations.

build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation

region filtering, FASTA sequence extraction and more.

It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.

to handle everything from small to very large projects with speed and efficiency.

scalable, and high performance remote function execution. Unlike centralized FaaS platforms, Globus Compute allows users to execute functions on heterogeneous remote computers, from laptops to campus clusters, clouds, and supercomputers. A Globus Compute endpoint is a persistent service launched by the user on a compute system to serve as a conduit for executing functions on that computer.

including OpenMPI for MPI support.

contains several hash-map implementations, including implementations that optimize for space or speed.

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.

(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.

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.

passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. - Homepage: http://software.intel.com/en-us/intel-mpi-library/

OpenMPI for MPI support, FlexiBLAS (Defaulting to OpenBLAS), FFTW and ScaLAPACK.

including OpenMPI for MPI support.

data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.

scalable concurrency support.

in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.

of target sequences using high-throughput sequencing reads.

in an ultra-fast manner using seed and extend.

providing much of the functionality present in LAPACK.

and debuggers

event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

conventions. This allows a programmer to call any function specified by a call interface description at run-time.

linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.

compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

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.

fully fledged Spatial SQL capabilities.

behind a consistent, portable interface.

exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.

The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.

toolchain developed for the Gnome project (but usable outside of the Gnome platform).

(but usable outside of the Gnome platform).

targeting Intel Architecture (x86).

performance multi threaded programs.

group MPI processes as an ordered set.

It features an extremely fast decoder, with speed in multiple GB/s per core.

LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.

DNA sequencing reads generated by Next-Generation Sequencing platforms.

by anchoring the information rich basecalling neural network output to a reference genome/transcriptome.

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%. .

parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression.

using data in the INSDC Sequence Read Archives.

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.

that runs (we hope) on almost any UN*X machine. ne is easy to use for the beginner, but powerful and fully configurable for the wizard, and most sparing in its resource usage.

and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

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.

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.

and several bioinformatic post-processing features

compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.

to maximize phylogenetic likelihood or posterior probability according to a reference alignment

is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.

for giant viruses and viruses that use alternative genetic codes.

a variety of online storage services

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.

It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

and manipulating data in SLOW5 format.

for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.

It annotates and predicts the effects of genetic variants (such as amino acid changes).

perform quality-control on BAM/CRAM/BCF/VCF/GVCF

which is used to generate consensus sequences

Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format

The purpose of swarm is to provide a novel clustering algorithm that handles massive sets of amplicons. Results of traditional clustering algorithms are strongly input-order dependent, and rely on an arbitrary global clustering threshold. swarm results are resilient to input-order changes and rely on a small local linking threshold d, representing the maximum number of differences between two amplicons.

take full advantage of multicore performance, that are portable, composable and have future-proof scalability.

sequence records for submission to GenBank

between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.

algorithm with a Voronoi cell parameterisation.

alignment.

into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.

into the H.265 AVC compression format, and is released under the terms of the GNU GPL.

is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.

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.