Description: A Fortran program for calculations on atoms and molecules in gas phase or solution. Used for diverse fields like molecular spectroscopy, organic and inorganic chemistry, crystallography, and pharmacochemistry.
AFNI (Analysis of Functional NeuroImages)
Description: A set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data.
AutoDock
Description: A suite of automated docking tools designed to predict how small molecules bind to a receptor of known 3D structure.
BLAST+
Description: A popular similarity search tool for sequence similarity searching, often providing the first evidence for the function of a newly sequenced gene or piece of sequence.
Bowtie
Description: An ultrafast, memory-efficient short read aligner for aligning large sets of short DNA sequences (reads) to large genomes.
Cufflinks
Description: A tool for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples.
Gaussian
Description: A state-of-the-art package for electronic structure modeling with capabilities for simulations in gas and solution phase.
HDF5 (Hierarchical Data Format 5)
Description: Organizes, stores, discovers, accesses, analyzes, shares, and preserves diverse, complex data in continuously evolving heterogeneous computing and storage environments.
IDL (Interactive Data Language)
Description: An interactive computer algebra system for algebraically manipulating unbounded integers, exact rational numbers, real numbers with arbitrary precision, symbolic formulae, polynomials, sets, lists, equations, arrays, vectors, and matrices.
Jaguar
Description: A high-performance ab initio package for both gas and solution phase simulations, with particular strength in treating metal-containing systems.
Maple
Description: An interactive computer algebra system for algebraically manipulating unbounded integers, exact rational numbers, real numbers with arbitrary precision, symbolic formulae, polynomials, sets, lists, equations, arrays, vectors, and matrices.
Mathematica
Description: A powerful 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.
Matlab
Description: A high-performance language for technical computing that provides support for a variety of statistical and graphical analyses.
Paraview
Description: A scalable, open-source visualization application for processing very large data in various data formats (structured and unstructured, time-varying and static).
R
Description: A language that bears a passing resemblance to the S language developed at AT&T Bell Laboratories, providing support for a variety of statistical and graphical analyses.
structure
Description: A free software package for using multi-locus genotype data to investigate population structure with applications like 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.
TopHat
Description: A fast splice junction mapper for RNA-Seq reads that 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 (Visual Molecular Dynamics)
Description: A molecular graphics program for interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes.