These were most of my products for the course CAP 6515 - Algorithms in Computational Biology
http://www.cs.ucf.edu/~shzhang/Combio11/index.html
In case the link goes away...
Reference Textbooks:
- P.A. Pevzner, Computational Molecular Biology: An Algorithmic Approach. The MIT Press, 2000 (CMB)
- D. Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press. 1997 (Dan)
O(n) Suffix trees and linear-z indexing are contained within