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ABySS ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.
ActivePerl ActivePerl is a distribution of Perl from ActiveState.
Admixture Admixture is a software tool for maximum likelihood of individual asncesdtries from mulitlocus SNP genotype datasets.
Anaconda Python Anaconda Python is a freemium open source distribution of the Python and R programming languages for large-scale data processing, predictive analytics, and scientific computing, that aims to simplify package management and deployment
Antlr Antlr is a powerful parser generator for reading, processing executing or translating structired text or binary files.
Apache 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 building of Java applications.
Atlas Atlas is an empirical tuning system that produces a BLAS library whihc has been specifically optimized for the platform you install Atlas on,
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.
Automake Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. Automake requires the use of Autoconf
BamTools BamTools is a C++ API and toolkit for analyzing and managing BAM files.
Bbmap BBMap is a short read aligner, as well as various other bioinformatic tools
Beast Beast is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
BEDTools Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks
Bfc Bfc (aka Breach) solves the coverability problem for multi-threaded programs.
BCFtools BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.
Binutils The GNU Binutils are a collection of binary tools, the main ones are ld - the GNU linker & as - the GNU assemble.
Bison Bison is a general-purpose generator that converts an annotated context-free grammer into a deterministic LR or generalized LR (GLR) parser employing LALR parser tables.
Blat Blat is a super-fast algorithim for finding near exact matches and as it handles most problems in memory it can handle genome-scale analyses very quickly.
Boost Boost provides free peer-reviewed portable C++ source libraries.
Bowtie Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning  large sets of short DNA sequences (reads) to large genomes.
Busco Busco privides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily informed expectations of gene content from near single-copy othologs selected from OrthoDV v9.
Bwa Bwa is a program for aligning sequencing reads against a large reference genome (e.g. human genome).
Bzip2 BZip2 is a free and open-source file compression program that uses the Burrrows-Wheeler algorithm. It only compresses single files and is not a file archiver.
Canu Canu is a single molecule sequencer assembler for genomes large and small.
Castep Castep is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materials proprieties including energetics, structure at the atomic level, vibrational properties, electronic response properties etc.
Cdat Cdat is plotting software used in atmospheric sciences and climatology.
Cdo Cdo is a large tool set for working on climate and NWP model data.
CMake CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method.
Comsol Comsol Multiphysics is a cross-platform finitie element analysis, solver and multiphysics simulation software.
Cuda Cuda is a parallel computing platform and application programming interface (API) model created by Nvidia.
Curl Curl is a command line tool and library for transferring data with URL syntax.
Delft3D Delft3D is a integrated 3D modelling framework for flows, sediment transport, waves, water quality, morphological developments and ecology in coastal, river, lake and estuarine areas.
Emboss Emboss is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
Expat

Expat is a stream-oriented XML parser library written in C. Axpat excels with files too large to fit RAM, and where performance and flexibility are crucial.

Fasta Fasta is a DNA and protein sequence alignment software package first described.
Fastqc Fastqc format is text-based format for storing both a biological sequence (usually nucleotide sequence) and it's corresponding quality scores.
Fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
Fastx_tool FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ file preprocessing.
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.
Ffmpeg Ffmpeg is 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 (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
Fgenes Fgenes provides pattern based human gene structure prediction (multiple genes, both chains).
Flex Flex is a fast lexical analyser generator. It is a tool for generating programs that perform pattern-matching on text. Flex is a free (but non-GNU) implementation of the original Unix lex program.
Freebayes Bayesian haplotype-based genetic polymorphism discovery and genotyping.
FragGeneScan FraGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.
GATK Developed in the Data Sciences Platform at the Broad Institute, GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.
Gaussian Gaussian is a general purpose computational chemistry software package.
Gb Taxonomy Tools Tools for measuring taxonomies.
Gcc Compiler system produced by the GNU Project supporting various programming languages.
Gdal Gdal is a translator library for raster and vector geospatial data formats that is released under an X/MIT style open source license by the Open Source Geospatial Foundation
Gemma GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS)
Ghostscript Ghostscript is an interpreter for the PostScript language and for PDF

Gmp
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.

Gnuplot
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. 
Grace Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif.
Grib-api Grib-api is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages
Gromacs Gromacs is a molecular dynamics package mainlky designed for simulations of proteins, lipids and nucleic acids.
Gsl The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
Hdf5 Hdf5 is a data model, library, and file format for storing and managing data.
Hmmer Hmmer is used for searching sequence databases for sequence homologs, and for making sequence alignments
Htslib Htslib is a C library for high-throughput sequencing data formats.

Idba
IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.
ImageMagick ImageMagick can be used to create, edit, compose or convert bitmap images.
Iris SciTools Iris based on Anaconda Python
ISMapper This program takes paired end Illumina short read sequence data, an IS query of interest and a reference genome or assembly and reports the locations of the IS query in the reference genome or the assembly.
Intel Compiler Intel C++ Compiler, also known as icc or icl, is a group of C and C++ compilers from Intel available for Windows, macOS, Linux and Intel-based Android devices.
JAGS JAGS is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
Java Java is a general-purpose computer programming language.
Jasper Jasper is an open source platform for developing always-on, voice- controlled applications.
Kaldi Kaldi is a speech recognition toolkit, freely available under the Apache License.
Kmer Analysis Toolkit (KAT) The Kmer Analysis Toolkit (KAT) is an Open Source tool developed at TGAC to work with Next Generation Sequencing (NGS) data.

Kraken
Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads.
Kronatools Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
Last LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads). 
Libgtextutils Gordon's text utils library.

Libtool
GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
Libxml Libxml is a freely licensed C language library for handling XML, portable across a large number of platforms.
Maker Maker is a portable and easily configurable genome annotation pipeline.
Matlab Matlab is a multi-paradigm numerical computing environment and fourth-generation programming language.  Details of running matlab in parallel can be found here.
Mawk Mawk is an interpreter for the AWK programming language.

Maxbin
Maxbin is an automatic tool for binning metagenomics sequences.
Megahit Megahit is an ultra-fast single-node solution for large and complex metagenomics assembly via succint de Bruijn graph.
Metabat Metabat is an efficient tool for accurately reconstructing single genomes from complex microbial communities.
MetaPhlAn MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution.
Mkl Mkl (Intel MKL) is a library of optimized math routines for science, engineering, and financial applications.

Mothur
Mothur is an open source software package for bioinformatics data processing. The package is frequently used in the analysis of DNA from uncultured microbes.
Mpc Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.
Mpfr Mpfr is a GNU portable C library for arbitarary-precision binary floating-point computation with correct rounding, based on GNU Multi-Precision Library.
Muscle Muscle couples heterogeneous computational multiscale models of multiple disciplines
Nag Nag provides methods for the solution of mathematical and statistical problems,
Namd Namd is computer software for molecular dynamics simulation.
NanoOk NanoOk is a tool for extraction, alignment and analysis of Nanopore reads.
Ncbi-blast Ncbi-blast finds regions of similarity between biological sequences.

Nco
The Nco toolkit manipulates and analyzes data stored in netCDF accesible formats.

Ncurses
Ncurses is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner.
Nektar Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers.
NetCDF NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
OpenBLAS OpenBLAS is an open source implementation of the BLAS (Basic Linear Algebra Subprograms) API with many hand-crafted optimizations for specific processor types
Openbugs Openbugs is a software package for performing Bayesian inference Using Gibbs Sampling.

OpenMPI
Open MPIis a Message Passing Interface (MPI) library project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI).
Openssl OpenSSL is a cryptography toolkit implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) network protocols and related cryptography standards required by them.
Org-Asm Org-Asm is the ORGanelle ASeMbler.
PatMaN PatMaN is a DNA pattern matcher for short sequences
Pbmpi Pbmpi is a Bayesian software for phylogenetic reconstruction using mixture models.
Pcre The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5
Perl Perl is a family of high-level, general purpose, interpreted, dynamic programming languages.
Pgi Pgi is the Portland Group Compiler.
PHEnix
PHEnix is Public Health England’s single nucleotide polymorphism calling pipeline
Picard Picard is a set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Platform MPI IBM Spectrum MPI is a high-performance, production-quality implementation of MPI designed to accelerate application performance in distributed computing environments.
Pplacer Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
Prodigal Prodigal is a microbial (bacterial and archaeal) gene finding program.
Prokka Prokka is a software tool for the rapid annotation of prokaryotic genomes.
Proj proj.4 is a standard UNIX filter function which converts geographic longitude and latitude coordinates into cartesian coordinates (and vice versa), and it is a C API for software developers to include coordinate transformation in their own software.
Pullseq Pullseq is a utility program for extracting sequences from a fasta/fastq file.
Pyferret PyFerret is a Python module wrapping Ferret. The pyferret module provides Python functions so Python users can easily take advantage of the Ferret's abilities to retrieve, manipulate, visualize, and save data.
R R is an open source programming language and software environment for statistical computing and graphics that is supported by the R Foundation for Statistical Computing
Raxml RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees
Readline

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.

RSEM 1.3.0 RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Ruby
Ruby is a dynamic, reflective, object-oriented, general-purpose programming language.
Samtools Samtools is a suite of programs for interacting with high-throughput sequencing data.
Schrodinger Schrodinger is a collection of software chemical or biochemical use
Singularity HPC Container system
Smalt SMALT aligns DNA sequencing reads with a reference genome.
Snpeff Snpeffis an open source tool that annotates variants and predicts their effects on genes by using an interval forest approach.
SPAdes SPAdes is an assembly toolkit containing various assembly pipelines.
Sparsehash Sparsehash is a memory-efficient C++ hash_map implementation.
Sra SRA toolkit contains important tools to manipulate SRA (Short Read Archive) file.

Stacks
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.

Staden
Staden is a a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin)
Stata Stata is a general-purpose statistical software package.

Szip
Szip is a freeware portable general purpose lossless compression program.
TensorFlow An open-source software library for Machine Intelligence
TeXLive TexLive is a free software distribution for the TeX typesetting system that includes major TeX-related programs, macro packages, and fonts.
Theano Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. 
Torch Torch is a deep learning framework with wide support for machine learning algorithms. It's open-source, simple to use, and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C / CUDA implementation.

Transdecoder
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
Transrate Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies.
Trimmomatic Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters.
TrimGalore TrimGalore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
Trinity 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.
Trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
Udunits The UDUNITS package from Unidata is a C-based package for the programatic handling of units of physical quantities.

Usearch
USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. 
Uvcdat Ultrascale Visualization Climate Data Analysis Tools
Vcftools VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project.

Velvet
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454.

Velvet-optimiser
Velvet is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
Visit VisIt is an open source, interactive, scalable, visualization, animation and analysis tool.
Vmd VMD is capable of working with very large structures up to the limits of available memory. The 64-bit versions of VMD allow large-size and long-timescale simulation trajectories to be loaded into physical memory and accommodate large volumetric datasets
Vsearch Vsearch provides high-throughput biological sequence analysis,
Weka Weka is a collection of machine learning algorithms for data mining tasks
Zlib Zlib is a software library used for data compression.