ArgoTree is a multiplatform (Java) application to draw phylogenetic trees read from NEXUS formatted data files. ArgoTree allows you to automatically color your phylogram to easily distinguish taxa and/or groups of taxa by setting up string matching rules. More...

O'Conner Consensus

This is a Java Application written by Benjamin Oswald to compute an O'Conner consensus for the purposes of search management. This application is free to use and distribute. Also posted is the source code. If you don't already have it, you will need to install the Java Runtime Environment (1.4 or later) Send any comments or suggestions to
To Use: download the file, change the extension from .zip to .jar, then just double click on the file and it should open.

O'Conner Consensus Java Application
Source Code

Polyploid Establishment and Evolution IBM's

This is a Java Application written by Benjamin Oswald to test hypotheses regarding polyploid establishment and evolution.

Executable Jar file: FTMsimulationsSt.jar
Initial parameters file: parameters.txt
Necessary Library BenjiTools.jar
Source Code (Zip File)

Source Code for Simulations with Inbreeding Depression Source Code IBD

PyroSNP (SNPparser and SNPviewer)

The SNPparser program parses the individual blocks (loci) in the 454AllDiffs file and identifies potential SNPs between the two mapped strains. Each potential SNP detected is assigned a “SNP score” ranging from 0 to 1 where a score of 0 indicates that a polymorphism occurs in the reads for each strain equally, and a score of 1 indicates that all the reads for each strain have a unique polymorphism. The specific algorithm is detailed in the PyroSNP documentation. Thus, the SNP score quantifies how consistently different samples are at this particular locus. Additionally, the PyroSNP application incorporates read quality information from the Roche454 output, allowing users to distinguish SNPs of low quality. The output from the PyroSNP parser application was then visualized using the SNPviewer application also developed to aid in SNP detection through complex sorting and the ability to view a potential SNP in its genetic context.

Download SNPparser  Download SNPviewer (and example data)

Vaccination Impact and Effectiveness simulations

These are web-based simulation models that make use of web-mathematica to provide advanced computation, hosted on University of Notre Dame servers

Vaccination Impact with age structured contact rates and spatial structure. This is a stochastic simulation of an age structured and spatially structured population using an SEIR model with vaccinations and parameterized with US census data.

Vaccine Effectiveness Simulations. These simulations estimate vaccine effectiveness given properties of the antigenic space over multiple years.