Listed here are software packages currently installed and maintained by CCR Staff. If additional applications are desired, please contact CCR Staff. The list below is organized by subject area.
For an alphabetical list of the software including compilers and numerical libraries (along with detailed user notes), please click here.
Contents
Bioinformatics
- iNquiry (Bioinformatics Web Portal)
- SeqWeb (Web Portal for GCG)
- BLAST (Basic Local Alignment Search Tool from NCBI)
- MPI-BLAST (Parallel MPI Version of BLAST)
- UCSC BLAT (Genome Browser)
- CS-ROSETTA (Sequence Analysis)
- GCG (Collection of Sequence Analysis Packages)
- HMMER (Protein Analysis Package)
- MPI-HMMER (Parallel MPI Version of HMMER)
- HYPHY (Phylogenetic Analysis Package)
- Ingenuity Pathways Analysis (Pathways Analysis Package)
- MRBAYES (Bayesian Interface of Phylogeny)
- PAML (Phylogenetic Analysis Package)
- PHYLIP (Phylogenetic Analysis Package)
- PhyML (Phylogenetic Analysis Package)
- PHRED/PHRAP (Sequence Assembly Software)
- PREPMS (MS Data Processing Tool)
- R (Statistical Package)
- ROSETTA (Sequence Analysis)
- SAGE (Statistical Analysis for Genetic Epidemiology)
- SOLAR (Sequential Oligogenic Linkage Analysis Routines)
- STRUCTURE (Genotype Analysis of Population Structure)
- VectorNTI (DNA and Protein Sequence Analysis)
Chemistry/Biochemistry
- WebMO (Web portal for GAMESS, GAUSSIAN, NWChem and Q-Chem)
- ADF (Quantum Chemistry Package)
- AMBER (Molecular Mechanics Package)
- AUTODOCK (Automatic Docking Tools)
- BABEL (File Format Conversion Utility)
- CHARMM (Molecular Mechanics Package)
- CNS (CNSsolve Crystallography & NMR System)
- CPMD (Car-Parrinello Molecular Dynamics)
- DALTON (Quantum Chemistry Package)
- DEMON (Quantum Chemistry Package)
- DOCK (Docking Package)
- DYNALIGN (RNA Sequence Analysis)
- GAMESS (Quantum Chemistry Package)
- GAUSSIAN94 (Quantum Chemistry Package)
- MOLEKEL (Molecular Visualization)
- MOPAC (Semiempirical Quantum Chemistry Package)
- NAMD(Molecular Dynamics Package)
- NMRPipe (Spectral Analysis Package)
- NWCHEM (Quantum Chemistry Package)
- QCHEM (Quantum Chemistry Package)
- TINKER (Molecular Mechanics Package)
- TOWHEE (Molecular Mechanics Package)
- TURBOMOLE (Quantum Chemistry Package)
- VMD (Visual Molecular Dynamics GUI)
Engineering
- CADENCE (Micro-chip Design Packages)
- CFX (Computational Fluid Dynamics Package)
- IDL (Data Visualization and Analysis Package)
- NETCDF (Data Formats and Libraries)
- PETSC (Portable Extensible Toolkit for Scientific Computation)
- STARCD (Computational Fluid Dynamics Package)
- TECPLOT (CFD and Numerical Simulation Visualization Package)