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
Tools
Package Comment
7zip Compression program which works with many formats
cvs Version control system
git Version control system
svn Version control system