| Package |
Version |
Application Area |
Official Website |
|
|
|
|
| ASE |
3.6.0 |
Atomistic Simulation Environment |
https://wiki.fysik.dtu.dk/ase/overview.html |
| Autodock |
4.2.3 |
Molecular Dynamics |
http://autodock.scripps.edu |
| Autodock Vina |
1.1.2 |
Molecular Dynamics |
http://vina.scripps.edu |
| BLAST |
2.2.24 |
Genomics, Bioinformatics |
http://blast.ncbi.nlm.nih.gov |
| CAESES-FFW |
3.0.19 |
CFD Analysis |
https://www.caeses.com/products/caeses-free/ |
| CMake |
2.8.9 |
Testing Tool |
http://www.cmake.org |
| CP2K |
2.3 |
Molecular Dynamics |
http://www.cp2k.org/about |
| CPLEX |
12.6.0 |
Optimization |
http://www-03.ibm.com/software/products/en/ibmilogcpleoptistud |
| Dakota |
6.1 |
Analysis and Optimization |
https://dakota.sandia.gov/ |
| EPOCH |
4.2.13 |
Plasma Physics |
http://www.ccpp.ac.uk/codes.html |
| FEBio |
2.4.2 |
Finite Element Analysis |
http://febio.org/ |
| FLUKA |
2011.2c-0 |
MonteCarlo |
http://www.fluka.org/fluka.php |
| fpocket |
2.0 |
Protein Cavity Detection |
http://fpocket.sourceforge.net/ |
| GAMESS |
2013125 |
Quantum Chemistry |
http://www.msg.chem.iastate.edu/gamess |
| GEANT4 |
4.9.6 |
Particle Simulations |
http://geant4.web.cern.ch/geant4/support/gettingstarted.shtml |
| GROMACS |
4.5.5 |
Molecular Dynamics |
http://www.gromacs.org |
| GPAW |
0.9.0 |
Electronic Structure |
http://wiki.fysik.dtu.dk/gpaw |
| HDF5 |
1.8.7 |
Portable Data Format |
http://www.hdfgroup.org/HDF5 |
| IOzone |
3.397 |
Benchmark Tool |
http://www.iozone.org |
| KlustaKwik |
3.0 |
Quantum Chemistry |
http://sourceforge.net/projects/klustakwik/ |
| LAMMPS |
16thFeb2016 |
Solid State Molecular Dynamics |
http://lammps.sandia.gov/ |
| Molden |
5.2 |
Quantum Chemistry Visualization |
http://www.cmbi.ru.nl/molden/ |
| MrBayes |
3.2.1 |
Phylogenetic and Evolutionary Models |
http://mrbayes.sourceforge.net/ |
| NAMD |
2.8 |
Molecular Dynamics |
http://www.ks.uiuc.edu/Research/namd |
| netCDF |
4.3.2 |
Data Manipulation |
http://www.unidata.ucar.edu/software/netcdf/ |
| NEURON |
7.3 |
Neuron Networks |
http://www.neuron.yale.edu/neuron/ |
| ns-3 |
3.24 |
Network Simulator |
https://www.nsnam.org/ |
| NWChem |
6.1 |
Computational Chemistry |
http://www.nwchem-sw.org/index.php/Main_Page |
| Octave |
3.6.1 |
Data Analysis & Visualization |
http://www.gnu.org/software/octave |
| Open Babel |
2.3.1 |
Chemical Data Toolbox |
http://sourceforge.net/projects/openbabel |
| OpenFOAM |
2.1.0 |
Computational Fluid Dynamics |
http://www.openfoam.com |
| OpenMD |
2.0 |
Molecular Dynamics |
http://openmd.org/ |
| Paraview |
3.12 |
Visualization |
http://www.paraview.org |
| Perl |
5.12.3 |
General purpose programming language |
http://www.perl.org |
| Placevent |
0.2 |
Molecular Dynamics |
http://sites.google.com/site/dansindhikara/Home/software/placement |
| Python |
2.7.1 |
General purpose programming language |
http://www.python.org |
| Qhull |
2012.1 |
Computational Geometry |
http://www.qhull.org |
| QIIME |
1.8.0 |
Bioinformatics |
http://www.qiime.org |
| QUANTUM ESPRESSO |
5.4.0 |
Quantum Chemistry |
http://www.quantum-espresso.org/ |
| R |
2.12.1 |
Statistical Computing Language |
http://www.r-project.org |
| Root |
5.34 |
Data Processing |
http://root.cern.ch/drupal/ |
| Su-2 |
4.2.0 |
Computational Fluid Dynamics |
http://su2.stanford.edu/ |
| Trinity |
2.0.6 |
RNA Sequencing |
https://github.com/trinityrnaseq/trinityrnaseq/wiki |
| VisIt |
2.10.2 |
Visualization and Analysis |
https://wci.llnl.gov/simulation/computer-codes/visit/ |
| VMD |
1.9.1 |
Molecular Dynamics Visualization |
http://www.ks.uiuc.edu/Research/vmd |
