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Application Owner Description
BLAST Open Source The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences and help identify members of gene families.
Bowtie Open Source Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at more than 25 million 35bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end.
BWA Open Source 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 other two are for longer sequences ranging from 70bp to 1Mbp.
ClustalW Open Source ClustalW is a general-purpose multiple alignment program for DNA or proteins. ClustalX is a graphical user interface for the ClustalW multiple-sequence alignment program.
FASTA Open Source FASTA is a more sensitive derivative of the FASTP program that can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence database by translating the DNA database as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. 
HMMER Open Source HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
MrBayes Open Source MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and amino acid sequences, restriction sites and standard binary data.
Phred Phrap Consed Commercial (Univ. Wash.) Phred is a base calling software with quality estimation; Phrap performs shotgun sequence assembly; and Consed is a sequence assembly editor companion to Phrap. Also available are Swat and CrossMatch, sequence alignment tools; and Phrapview, a graphical tool that provides a "global" view of the Phrap assembly, complementary to the "local" view provided by the Consed.
SOAP Open Source SOAP provides a full solution to next generation sequencing data analysis. It consists of a new alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder (SOAPindel ), a structural variation scanner (SOAPsv) and a de novo short reads assembler (SOAPdenovo).
Velvet Open Source Velvet performs de novo short read assembly using de Bruijn graphs. It can be used for Solexa and 454 sequencing data assembly.
Application Owner Description
AutoDock Open Source AutoDock is a suite of automated docking tools that predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3-D structure.
DOCK6 Commercial (UCSF ) DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.
FlexX Commercial (BioSolveIT) Predicts protein-ligand interactions.
GLIDE Commercial (Schrödinger) A complete solution for ligand-receptor docking, from virtual screening of millions of compounds to binding mode predictions.
GOLD Open Source Gold calculates the docking modes of small molecules into protein binding sites.
ICM Commercial (molsoft) A desktop-modeling environment for molecular structure and function.
LigandFit Commercial (Accelrys ) Code for docking ligands into protein active sites. The method employs a cavity detection algorithm for detecting invaginations in the protein as candidate active site regions.
ROCS Commercial (OpenEye) ROCS is a virtual screening tool that can identifies potentially active compounds by shape comparison. 
Application Owner Description
ABINIT Open Source Main program helps users 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 or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on density-functional perturbation theory, and many more properties. 
BigDFT Open Source BigDFT is a DFT massively parallel electronic structure code (GPL license) using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh. GTH or HGH pseudopotentials are used to remove the core electrons. With a Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions.
CASTEP Commercial (Accelrys ) CASTEP is a code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of material properties including energetics, structure at the atomic level, vibrational properties and electronic response properties. Offers a wide range of spectroscopic features that link directly to experiment, such as infrared and Raman spectroscopies, NMR and core level spectra.
CP2K Open Source CP2K performs atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as density functional theory using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials.
CPMD Open Source The CPMD code is a parallelized plane wave/pseudopotential implementation of density functional theory, particularly designed for ab-initio molecular dynamics.
DMol3 Commercial (Accelrys ) DMol3 is a commercial (and academic) software package that uses density functional theory with a numerical radial function basis set to calculate the electronic properties of molecules, clusters, surfaces and crystalline solid materials from first principles. It can either use gas phase boundary conditions or 3-D periodic boundary conditions for solids or simulations of lower dimensional periodicity. 
LAMMPS Open Source Large-scale atomic/molecular massively parallel simulator (LAMMPS) is a classical molecular dynamics code.
SIESTA Open Source (commercial version from Nanotec) SIESTA is both a method and its computer program implementation for performing electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA uses strictly localized basis sets and linear-scaling algorithms that can be applied to suitable systems. The code can be used for a wide range of applications, from quick exploratory calculations to simulations that match other approaches, such as plane-wave and all-electron methods.
VASP Commercial (Univ. of Vienna) VASP performs ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.
Application Owner Description
Mascot Commercial (Matrix Science) Mascot is a mass spectral search algorithm that uses mass spectrometry data to identify proteins from primary sequence databases.
OMSSA Open Source Mass spectrometry software used for data acquisition, analysis or representation.
Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments.
SEQUEST Open Source SEQUEST correlates uninterpreted tandem mass spectra of peptides with amino acid sequences from protein and nucleotide databases. It will determine the amino acid sequence and thus the protein(s) and organism(s) that correspond to the mass spectrum being analyzed.
X!Tandem Open Source X! Tandem can match tandem mass spectra with peptide sequences. It generates theoretical spectra for peptide sequences using information about intensity associated with amino acids. These spectra are compared with experimental data to generate an expectation value as a threshold score.
Application Owner Description
ACEMD Acellera
ACEMD is a heavily optimized molecular dynamics engine specially designed to run on NVIDIA GPUs. 
AMBER Open Source Assisted model building with energy refinement (AMBER) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs), and a package of molecular simulation programs which includes source code and demos. 
CHARMM Commercial (Accelrys ) CHARMM (Chemistry at HARvard Molecular Mechanics) is the academic version of the CHARMM simulation program available through Harvard. CHARMM uses empirical energy functions to describe the forces on atoms in molecules.
DESMOND D.E. Shaw Research
DESMOND performs high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques and can run on platforms containing a large number of processors, or on a single computer.
GAMESS Open Source General atomic and molecular electronic structure system (GAMESS) is a general ab initio quantum chemistry package. It can compute wave functions ranging from RHF, ROHF, UHF, GVB and MCSCF, with CI and MP2 energy corrections available for some of these.
Gaussian Commercial (Gaussian) Gaussian 09 provides electronic structure modeling, and is licensed for a wide variety of computer systems.
GROMACS Open Source GROMACS performs molecular dynamics, simulating the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules such as proteins, lipids and nucleic acids that have complicated bonded interactions, but is also being used for research on nonbiological systems, such as polymers.
Jaguar Commercial (Schrödinger) Jaguar is an ab initio package for both gas and solution phase simulations, with particular strength in treating metal containing systems.
LAMMPS Open Source Large-scale atomic/molecular massively parallel simulator (LAMMPS) is a classical molecular dynamics code.
MOLPRO Commercial (University College Cardiff Consultants Ltd.) Molpro is a complete system of ab initio programs for molecular electronic structure calculations. The emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods.
NAMD Open Source NAMD is a parallel molecular dynamics code designed for simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms.
NWChem Open Source NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum mechanical descriptions of the electronic wave function or density. NWChem can perform classical molecular dynamics and free energy simulations. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.
Q-Chem Commercial (Q-Chem) Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from DFT/HF calculations to post-HF correlation methods.
MPACK is a Fortran program package that involves scattering problems of two octet baryons by the quark-model interactions, fss2 and FSS (fssG.f), and their applications to the Faddeev calculations for the triton (triton.f) and the hypertriton (hypt.f).
Terachem Commercial (PetaChem) TeraChem is general-purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system.