High Performance Computing Collaboratory
Applications
A number of applications are in use on the cluster. Many are free but some applications may require a licensing fee for new users. Contact us if you have questions about a specific applications. Please choose a category of applications below:
Biology
MrBayesMrBayes is a program for the Bayesian estimation of phylogeny. Bayesian
inference of phylogeny is based upon a quantity called the posterior probability
distribution of trees, which is the probability of a tree conditioned
on the observations. The conditioning is accomplished using Bayes's theorem.
The posterior probability distribution of trees is impossible to calculate
analytically; instead, MrBayes uses a simulation technique called Markov
chain Monte Carlo (or MCMC) to approximate the posterior probabilities
of trees.
MrBayes Home Page
Using MrBayes on the Cluster
PAUP* provides tools for inferring and interpreting phylogenetic trees.
You can analyze molecular sequences, morphological data and other data
structures using maximum likelihood, parsimony and distance methods.
PAUP* Home Page
Using PAUP* on the Cluster
Chemistry
Gaussian 98Gaussian 98 is the latest in the Gaussian series of electronic structure
programs. It is designed to model a broad range of molecular systems under
a variety of conditions, performing its computations starting from the
basic laws of quantum mechanics. Gaussian 98 was written to take advantage
of the Linda programming environment (see the Resources page).
Gaussian 98 Home Page
Economics
GaussThe GAUSS Mathematical and Statistical System is a fast matrix programming
language widely used by scientists, engineers, statisticians, biometricians,
econometricians, and financial analysts.
Gauss Home Page
Graphics
PVMPOVPVMPOV is a version of the popular POVRAY (Persistence of Vision Raytracing)
program that has been updated to include PVM support (see Resources page)
so that it can take advantage of the resources provided by a cluster.
Please note that this version of the POVRAY is not supported by the makers
of the original POVRAY. Nevertheless, all of the features of POVRAY are
also present in PVMPOV.
POVRAY Home Page