• Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use 
• Provides high-level syntax (API) deliberately similar to Matlab 
• Useful for algorithm development directly in C++, or quick conversion of research code into production environments (eg. software & hardware products) 
• Can be used for machine learning, pattern recognition, computer vision, signal processing, bioinformatics, statistics, finance, etc 
• Provides efficient classes for vectors, matrices and cubes (1st, 2nd and 3rd order tensors), as well as 200+ associated functions; integer, floating point and complex numbers are supported 
• Various matrix decompositions are provided through integration with LAPACK, or one of its high performance drop-in replacements (eg. multi-threaded Intel MKL, orOpenBLAS) 
• A sophisticated expression evaluator (based on template meta-programming) automatically combines several operations to increase speed and efficiency 
• Can automatically use OpenMP multi-threading (parallelisation) to speed up computationally expensive operations

Tool for automation of building and testing software. 

BEAST1

BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. 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. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

BEAST 2

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.

Boost provides free peer-reviewed portable C++ source libraries.

We emphasize libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

We aim to establish "existing practice" and provide reference implementations so that Boost libraries are suitable for eventual standardization. Ten Boost libraries are included in the C++ Standards Committee's Library Technical Report (TR1) and in the new C++11 Standard. C++11 also includes several more Boost libraries in addition to those from TR1. More Boost libraries are proposed for standardization in C++17.

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Cairo is a 2-D 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.

Cairo is designed to produce consistent output on all output media while taking advantage of display hardware acceleration when available (e.g., through the X Render Extension).

The Cairo API provides operations similar to the drawing operators of PostScript and PDF. Operations in cairo including stroking and filling cubic Bézier splines, transforming and compositing translucent images, and antialiased text rendering. All drawing operations can be transformed by any affine transformation (scale, rotation, shear, etc.)

Cairo is implemented as a library written in the C programming language, but bindings are available for several different programming languages.

CMake is an open-source, cross-platform family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice. The suite of CMake tools were created by Kitware in response to the need for a powerful, cross-platform build environment for open-source projects such as ITK and VTK.

Curl is used in command lines or scripts to transfer data. It is also used in cars, television sets, routers, printers, audio equipment, mobile phones, tablets, settop boxes, media players and is the internet transfer backbone for thousands of software applications affecting billions of humans daily.

DL_POLY is a general purpose classical molecular dynamics simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.

• Eigen is versatile.
  • It supports all matrix sizes, from small fixed-size matrices to arbitrarily large dense matrices, and even sparse matrices.
  • It supports all standard numeric types, including std::complex, integers, and is easily extensible to custom numeric types.
  • It supports various matrix decompositions and geometry features.
  • Its ecosystem of unsupported modules provides many specialized features such as non-linear optimization, matrix functions, a polynomial solver, FFT, and much more.
• Eigen is fast.
  • Expression templates allow to intelligently remove temporaries and enable lazy evaluation, when that is appropriate.
  • Explicit vectorization is performed for SSE 2/3/4, AVX, FMA, AVX512, ARM NEON (32-bit and 64-bit), PowerPC AltiVec/VSX (32-bit and 64-bit) instruction sets, and now S390x SIMD (ZVector) with graceful fallback to non-vectorized code.
  • Fixed-size matrices are fully optimized: dynamic memory allocation is avoided, and the loops are unrolled when that makes sense.
  • For large matrices, special attention is paid to cache-friendliness.
• Eigen is reliable.
  • Algorithms are carefully selected for reliability. Reliability trade-offs are clearly documented and extremely safe decompositions are available.
  • Eigen is thoroughly tested through its own test suite (over 500 executables), the standard BLAS test suite, and parts of the LAPACK test suite.
• Eigen is elegant.
  • The API is extremely clean and expressive while feeling natural to C++ programmers, thanks to expression templates.
  • Implementing an algorithm on top of Eigen feels like just copying pseudocode.
• Eigen has good compiler support as we run our test suite against many compilers to guarantee reliability and work around any compiler bugs. Eigen also is standard C++98 and maintains very reasonable compilation times.

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).

The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.

However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results.

The FASTX-Toolkit tools perform some of these preprocessing tasks.

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.

GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar corrections, with various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code.

A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered.

Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolplt program (for Macintosh, Windows, or Linux desktops), are available for viewing of the final results, and the Avogadro program can assist with preparation of inputs.

Summary

Gaussian 09 is the latest version of the Gaussian^® series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).

Gaussian 09 provides the most advanced modeling capabilities available today, and it includes many new features and enhancements which significantly expand the range of problems and systems which can be studied. With Gaussian 09, you can model larger systems and more complex problems than ever before, even on modest computer hardware.

Description

Gaussian 09 is the latest version of the Gaussian^® series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).

Gaussian 09 provides the most advanced modeling capabilities available today, and it includes many new features and enhancements which significantly expand the range of problems and systems which can be studied. With Gaussian 09, you can model larger systems and more complex problems than ever before, even on modest computer hardware.

Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.

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.

• Automation - gulp is a toolkit that helps you automate painful or time-consuming tasks in your development workflow.
• Platform-agnostic - Integrations are built into all major IDEs and people are using gulp with PHP, .NET, Node.js, Java, and other platforms.
• Strong Ecosystem - Use npm modules to do anything you want + over 2000 curated plugins for streaming file transformations
• Simple - By providing only a minimal API surface, gulp is easy to learn and simple to use

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. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.

HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent.

Intel Fortran Compiler, also known as IFORT, is a group of Fortran compilers from Intel.

Java is at the heart of our digital lifestyle. It's the platform for launching careers, exploring human-to-digital interfaces, architecting the world's best applications, and unlocking innovation everywhere—from garages to global organizations.

Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano. It was developed with a focus on enabling fast experimentation. Being able to go from idea to result with the least possible delay is key to doing good research.

Use Keras if you need a deep learning library that:

• Allows for easy and fast prototyping (through user friendliness, modularity, and extensibility).
• Supports both convolutional networks and recurrent networks, as well as combinations of the two.
• Runs seamlessly on CPU and GPU.

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java™.

mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community. 

The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0 (SVr4), 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 SVr4-curses enhancements over BSD curses. SVr4 curses became the basis of X/Open Curses.

Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).

Oases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.

OpenCV (Open Source Computer Vision Library) is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware acceleration of the underlying heterogeneous compute platform.

Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 14 million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advanced robotics.

The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation.

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

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 2,500 basis functions running serially or in parallel.

Welcome to the home of pyMPI, a project integrating the Message Passing Interface (MPI) into the Python interpreter. pyMPI is being developed primarily by researchers at Lawrence Livermore National Laboratory.

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

FYI: For more information about R, visit the Data and Statistical Analysis Index of Articles in Research Matters.

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.

The history facilites are also placed into a separate library, the History library, as part of the build process. The History library may be used without Readline in applications which desire its capabilities.

Readline is free software, distributed under the terms of the GNU General Public License, version 3. This means that if you want to use Readline in a program that you release or distribute to anyone, the program must be free software and have a GPL-compatible license.

If you would like advice on making your license GPL-compatible, contact licensing@gnu.org.

SAM, Sequence Alignment Map, format is a generic format for storing large nucleotide sequence alignments.

• Simple and efficient tools for data mining and data analysis
• Accessible to everybody, and reusable in various contexts
• Built on NumPy, SciPy, and matplotlib
• Open source, commercially usable - BSD license

SPADES is an assembly toolkit containing various assembly pipelines.

SPADES works with Illumina or IonTorrent reads, and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.

SPADES supports paired-end reads, mate-pairs and unpaired reads. It can take as input several paired-end and mate-pair libraries simultaneously. SPADES was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPADES is not intended for larger genomes, such as mammalian size genomes. For such purposes, you use SPADES at your own risk.

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.

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).

TensorFlow™ is an open-source software library for numerical computation using data-flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API. TensorFlow was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.

Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, 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.

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.

Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.