# Research

(local content)

- Papers
My PhD thesis, and research papers I have co-authored.
- Java Sequence Alignment Demo
A java applet demonstrating how a number of different sequence alignment algorithms compute an optimal alignment between two sequences. The demo is animated on a 2d matrix showing which cells of the matrix are computed by the selected algorithm.

### Sequence Alignment and Analysis

(content at Monash University.
Courtesy of Lloyd
Allison)

- Various
Alignment Algorithm Implementations
Various software for sequence alignment from my PhD thesis and subsequent work. Implemention language varies between C, C++ and Python.
- M-alignment
An implemention of a probabilistic alignment algorithm for low-entropy sequences. Implemented in Java.
- A
DNA compression program
An implementation of a DNA compression algorithm based on a model of approximate repeats. Implemented in Java.