Software and Tools
[Computational Structural Analysis][Quantum Chemistry] [Semiempirical][Molecular Mechanics / Dynamics] [Crystallography and Materials Science] [Computational Fluid Dynamics] [Math and Statistics] [Compilers & Programming] [Visualization] [Supported Operating Systems] [Bioinformatics] [Other Simulations]
Computational Structural Analysis
Finite element analysis program for structural mechanics. Both Abaqus/Standard and Abaqus/Explicit are available. *
Graphic interface for use with engineering software packages. *
Quantum Chemistry
CPMD
The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
The General Atomic and Molecular Electronic Structure System is an ab initio quantum chemistry code.
GAUSSIAN 03The pre-eminent ab initio quantum mechanics package. Gaussian has a very large range of quantum mechanical methods.
Allows reaction rates to be computed using the Gaussian software package.
JAGUARHigh performance quantum mechanics package. Jaguar scales more favorably to large numbers of atoms than many other ab initio codes. *
JuNoLoJuNoLo is a parallel code that implements vdW-DF theory. The code works as a postprocessing tool using the charge density obtained from some Density Functional Theory code.
Multilevel is a program for doing dual-level and multi-level computations. *
A highly parallelized package for quantum chemistry and molecular dynamics.
ORCA is a flexible, reasonably efficient and easy-to-use general purpose tool for quantum chemistry 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 correlated ab initio methods. It can also treat environmental and relativistic effects. *
POLYRATE computes chemical reaction rates using variational or conventional transition state theory. POLYRATE is designed to compute additional information using data generated by other programs as its input. (e.g., the results computed by GAMESS or Gaussian can be used as the input to POLYRATE).
The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and multi-reference configuration interaction models. Molecular point-group symmetry is utilized throughout to maximize efficiency.
The Quantum-ESPRESSO package contains software for Density-Functional Theory calculations using a Plane-Wave basis sets and pseudopotentials.
Semiempirical
AMSOL
Semiempirical chemistry code designed to model molecules in solution. *
MOPACMOPAC is a general purpose, semi-empirical molecular orbital program for the study of chemical reactions involving molecules, proteins, ions, and linear polymers.
Molecular Mechanics / Dynamics
Amber stands for "Assisted Model Building with Energy Refinement". It is a suite of packages for running molecular dynamics and mechanics simulations.*
AutodockAutoDock 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 known 3D structure.
DesmondDesmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters.
GROMACSThe GROMACS developers claim that it is the world's fastest molecular dynamics program.
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code.
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
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Crystallography and Materials Science
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis.
CCP4Crystallography & NMR structure determination package. *
CNSCrystallography & NMR structure determination package. *
Crystallography & NMR structure determination package.*
Computational Fluid Dynamics
Code_Saturne is a public domain CFD program.
CGNS (CFD General Notation System) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.
CFD-ACE+ is an advanced CFD & multiphysics software package. It enables
coupled simulations of fluid, thermal, chemical, biological, electrical and
mechanical phenomena. CFD-FASTRAN is a leading commercial CFD software for
aerodynamic and aerothermodynamic applications. It employs state-of-the-art
multiple moving body capability for simulating most complex aerospace problems
including missile launch, maneuvering and staging, and aircraft flight dynamics
and store separation. *
The INS2D/INS3D codes solve the incompressible Navier-Stokes equations in two-dimensional/three-dimensional generalized coordinates for both steady-state and time varying flow. The equations are formulated into a hyperbolic set of PDE using the method of artificial compressibility. The convective terms are differenced using an upwind biased flux-difference splitting. The equations are solved using an implicit line-relaxation scheme. The code is written for single or multiple-zone calculations. It can utilize either pointwise continious zonal interfaces, or random overlapped zonal interfaces if a PEGASUS interpolation database is supplied. The flow solver contains pre-coded boundary conditions for slip and noslip walls, symmetry planes, inflow and outflow boundaries, and far-field boundaries.
A fluid dynamics program for modeling weather patterns.
WRF
A fluid dynamics program for modeling weather patterns.
SCOTCH is a software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
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Math and Statistics
The AMD Core Math Library (ACML) incorporates BLAS, LAPACK and FFT routines, which are designed to obtain excellent performance running on AMD platforms.
deal.IIdeal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.
f2cblaslapackFortran-to-C blas & lapack libraries.
IMSLThe IMSL Libraries are a comprehensive resource of more than 900 FORTRAN mathematical and statistical subroutines for scientists, engineers, and mathematicians.
LAPACK++ is a library for high performance linear algebra computations.
METISMETIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.
MKLA thread-safe math library from Intel.
OctaveA high-level interactive language for numerical computations. CLICK HERE for compatability information.
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
R is a language and environment for statistical computing and graphics.
SCSLMath library from SGI, which uses mpt parallelization.
SLATECSLATEC is a math library that supports such calculations as: arithmetic, error analysis; elementary and special functions; elementary vector operations; solutions of systems of linear equations; and much more.
TrilinosThe Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.
Compilers & Programming
Assembler
GNU assembler.
C/C++C and C++ compilers from GNU and Intel.
CxxTest is a C++ unit test harness that was highly recommended by several reviewers.
Fortran 77 & Fortran 90
Fortran compilers from GNU and Intel.
GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages.
gprofGNU code profiling tool.
GNU Common LISP is an open source implementation of Common LISP. It produces native object code by first generating C code and then calling a C compiler.
MPIMessage passing libraries are available for messaging over NUMA-link and infiniband connections.
Objective Caml is an object-oriented extension of the Caml language. It has both a native compiler and a bytecode compiler.
ompP
ompP is a profiling tool for OpenMP applications written in C/C++ or FORTRAN.
OpenMP
OpenMP is a means for creating shared memory parallel programs through the use of compiler directives and OpenMP capable compilers.
Perl, python, awk, tk, tclUnix scripting languages.
Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.
A software tool for debugging and profiling of parallel software.
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Visualization
Blender
Blender is a free open source 3D content creation suite.
Circos is a software package for visualization, which is popular for displaying biological data.
FigureGenFigureGen is a program for generating graphics from ADCIRC.
gnuplotA portable command-line driven interactive datafile (text or binary) and function plotting utility.
GMTGMT (Generic Mapping Tools) is a collection of programs for manipulating geographic and Cartesian data sets.
GraceA WYSIWYG 2D plotting tool for the X Window system.
NCAR GraphicsA set of FORTRAN library routines for generating graphics from a user application.
Treeviz is a graphical program for visualization of large tree structures.
VMDVMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
XCrySDenXCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
Supported Operating Systems
Linux
Bioinformatics
AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
BEAST is a phylogenetic analysis program.
Bowtie is an ultrafast, memory-efficient short read aligner.
CAP3CAP3 Sequence assembly program.
A general purpose multiple sequence alignment program for DNA or proteins.
Cufflinks is a reference-guided assembler for RNA-Seq experiments. It simultaneously assembles transcripts from reads and estimates their relative abundances, without using a reference annotation.
GARLIGARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned sequence datasets using the maximum-likelihood criterion.
Genome Analysis ToolkitThe Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers.
KarmaKarma is a high speed aligner for mapping FASTQ reads to a reference genome.
MAFFTMAFFT is a multiple sequence alignment program.
MaqMaq stands for Mapping and Assembly with Quality. It builds an assembly by mapping short reads to reference sequences. Maq was previously known as mapass2.
Mothur is a bioinformatics program designed to meet the needs of the microbial ecology community.
A parallel version of NCBI BLAST.
MrBayes is a program for the Bayesian estimation of phylogeny.
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
A suite of bioinformatics utilities, including NCBI BLAST.
NEXUS Class LibraryThe Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.
PHASEThe program PHASE implements methods for estimating haplotypes from population genotype data.
PhyloBayesPhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.
RANDFOLDRANDFOLD is software that computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.
RAxMLRAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood [1] based inference of large phylogenetic trees.
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. *
RNA2MAPThis tool can be used to perform whole genome analysis of SOLiD RNA library reads. It consists of three major procedures: filtering, matching against miRBase sequences (Sanger), and matching against a reference genome.
SHRiMPSHRiMP stands for SHort Read Mapping Package. SHRiMP is a software package for aligning genomic reads against a target genome.
SQUIDSQUID is a library of C functions and utility programs for sequence analysis.
TopHatTopHat is a splice junction mapper for short RNA-Seq reads.
TRFTandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
Twinscan finds genes in a "target" genomic sequence by simultaneously maximizing the probability of the gene structure in the target and the evolutionary conservation dervied from "informant" genomic sequences.
UMFPACKUMFPACK is a set of routines for solving sparse linear systems via LU factorization.
VelvetVelvet is a sequence assembler for very short reads.
Vienna RNA is a program for RNA secondary structure prediction and comparison.
A program for searching databases of DNA and protien sequences. *
Other Simulations
Kintecus
Kintecus is a powerful Industrial Strength/Research Grade chemical modeling software for simulation of combustion, nuclear, biological, enzyme, atmospheric and many other chemical kinetic and equilibrium processes.
M5 is a modular platform for computer system architecture research, encompassing system-level architecture as well as processor microarchitecture.
NS-2Ns is a discrete event simulator targeted at networking research. Ns provides substantial support for simulation of TCP, routing, and multicast protocols over wired and wireless (local and satellite) networks.
Sim-AlphaSim-Alpha is a processor architecture simulator based on SimpleScalar that implements a validated model of the Alpha 21264 processor.
* Commerical users and academic researchers doing work under contract to commercial customers must pay an additional fee for the use of this software.