ADF ADF (Amsterdam Density Functional) is a Fortran program for calculations on atoms and molecules (in gas phase or solution). It can be used for the study of such diverse fields as molecular spectroscopy, organic and inorganic chemistry, crystallography, and pharmacochemistry.
afni AFNI (which might be an acronym for Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data – a technique for mapping human brain activity.
AutoDock AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualized. This can help, for example, to guide organic synthetic chemists to design better binders.
BLAST+ Sequence similarity searching is one of the more important bioinformatics activities and often provides the first evidence for the function of a newly sequenced gene or piece of sequence. Basic Local Alignment Search Tool (BLAST) is probably the most popular similarity search tool.
Bowtie Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35 base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or colorspace alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers.
Cufflinks Cufflinks assemble transcripts, estimates their abundances, and test for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimate the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Gaussian Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian is licensed for a wide variety of computer systems. All versions of Gaussian contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.
HDF5 The HDF5 technology suite is designed to organize, store, discover, access, analyze, share, and preserve diverse, complex data in continuously evolving heterogeneous computing and storage environments. HDF5 supports all types of data stored digitally, regardless of origin or size. Petabytes of remote sensing data collected by satellites, terabytes of computational results from nuclear testing models, and megabytes of high-resolution MRI brain scans are stored in HDF5 files, together with metadata necessary for efficient data sharing, processing, visualization, and archiving.
IDL IDL, the Interactive Data Language, is the ideal software for data analysis, visualization, and cross-platform application development. IDL integrates a powerful, array-oriented language with numerous mathematical analysis and graphical display techniques, thus giving you incredible flexibility.
Jaguar Jaguar is a high-performance ab initio package for both gas and solution phase simulations, with particular strength in treating metal-containing systems, making it the most practical quantum mechanical tool for solving real-world problems.
Maple Maple is an interactive computer algebra system. Maple  can algebraically manipulate unbounded integers, exact rational numbers, real numbers with arbitrary precision, symbolic formulae, polynomials, sets, lists, equations, arrays, vectors, and matrices.  It can solve systems of  equations and differentiate and integrate expressions.
Mathematica At the core of Mathematica is its highly developed symbolic language, which unifies a broad range of programming paradigms, and uses its unique concept of symbolic programming to add a new level of flexibility to the very concept of programming.
Matlab MATLAB is a high-performance language for technical computing that integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation.
Paraview ParaView is a scalable, open-source visualization application. When run in a parallel environment, ParaView can process very large data in a wide variety of data formats (structured and unstructured, time-varying and static). It provides a comprehensive suite of visualization algorithms and supports many different file formats for both loading and exporting datasets. This application is extensible, so new algorithms can be easily added.
R R is a language that bears a passing resemblance to the S language developed at AT&T Bell Laboratories.  It provides support for a variety of  statistical  and graphical analyses.  R is a true computer language that contains a number of control-flow constructions for iteration and alternation.  It allows users to add additional functionality by defining new functions.
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. It can be applied to most of the commonly-used genetic markers, including SNPs, microsatellites, RFLPs, and AFLPs.
TopHat TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra-high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
VMD VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes.