Application Software

Scientific Software
Package Comment
BEAST Biology: Tools for Bayesian MCMC analysis of molecular sequences
Biopython Biology: Tools for biological computation
CROP Biology: Tool for metagenomics studies
CP2K Chemistry/Physics: Molecular dynamics program
Desmond Chemistry/Physics: Molecular dynamics program
FreeSurfer Neuroscience: Set of analysis tools for FMRI- and MRI-Data
FSL Neuroscience: Analysis tool for FMRI-, MRI- and DTI-Data
GAUSSIAN Chemistry: Electronic structure modelling tool
Gauss View Chemistry: Input preparation for and display of Gaussian results
GROMACS Chemistry: GROMACS is a versatile package to perform molecular dynamics
Gnuplot General: Graphing tool
LAMMPS Chemistry/Physics: Molecular dynamics program
MATLAB General: Numerical computing environment
MIRA Biology: Sequence assembly software
Molden Chemistry: Input preparation for and display of QM software results
mothur Biology: Molecular data analysis for microbial ecologists
MrBayes Biology: Bayesian inference software for phylogeny
NAMD Chemistry/Physics: Parallel molecular dynamics program
NBO/NBOView Chemistry: Analysis and visualisation of bonds - currently unavailable
Netlogo Various: General simulation tool
Octave General: Language for solving mathematical problems numerically
OOMMF Physics: Micromagnetics simulation program
ORCA Chemistry: General purpose tool for quantum chemistry
PHENIX Chemistry/Physics: Software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods
Quantum Espresso Chemistry/Physics: Code for electronic-structure calculations
R Statistics: Programming environment and software environment for statistical calculations and graphics
RAxML Biology: Sequential and parallel Maximum Likelihood based inference of large phylogenetic trees
SymeTREE Biology: Phylogenetic analysis software
Turbomole Chemistry: Calculation of molecular wave functions
VASP Chemistry/Physics: Program for performing ab initio quantum mechanical molecular dynamics
Wien2k Chemistry/Physics: Program for performing electronic structure calculations using DFT
Package Comment
7zip Compression program which works with many formats
cvs Version control system
git Version control system
svn Version control system