Useful References for CSE 300, Fall 2007

Yufeng Wu


The following lists a number of other references that may be of potential interests.

Latex

This web page  provide good information for people new to Latex.

String algorithms and applications

1. The original Landau and Schmidt paper on tandem repeat detection can be found from here.
2. Read this paper for a different perspective about trandem repeat, by Gary Benson (PDF).

Multiple Sequence Alignment

Unfortunately, I could not find on-line links to one of the following papers.

1. Pevzner's paper on improving the MSA approximation: can be found here (Link).
2. Bafna, et al. improved the approxmation algorithm further in: Approximation algorithms for multiple sequence alignment,
Theoretical Computer Science, 1997.

Phylogeny

On multi-state perfect phylogeny

1. A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies (Link),
 Sampath Kannan, Tandy Warnow, 1996.
2. A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States Is Fixed (Link),
Richa Agarwala, David Fernández-Baca, 1994.