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