Software

The text book Introduction to Computational Biology: An Evolutionary Approach comes with the bioinformer software, which illustrates a number of data structures and algorithms commonly used in bioinformatics. The following sections contain links to additional programs developed by us that implement ideas treated in the main text.

Chapter 3

Suffix Trees

1. drawStrees: Program for interactively drawing generalized suffix trees.
2. shustring: Program for identifying shortest unique substrings (=shustrings) in DNA or protein sequences.

Keyword Trees

• medMatch: Program for generating a gene index of Medline.

Chapter 7

1. Pattern Scanning with Profiles
2. SGP-1: Syntenic Gene Prediction Program
3. gff2aplot: Pair-wise alignment-plots for genomic sequences in PostScript/

Chapter 11

1. drawWrightFisher: Program for visualizing evolution in a Wright-Fisher population.
2. coalator: Program for drawing random gene genealogies.
3. drawGenealogy: Program for drawing random family histories.

Chapter 12

• LIAN: Program for testing the null hypothesis of linkage equilibrium in multi-locus data.