## 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

MrBayes
MrBayes 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***
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 98
Gaussian 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

Gauss
The 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

PVMPOV
PVMPOV 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