A Reduction Algorithm for Computing The Hybridization Number of Two Trees

• Main Authors: Magnus Bordewich, Simone Linz, Katherine St. John, Charles Semple
• Format: Article
• Language: English
• Published: SAGE Publishing 2007-01-01
• Series: Evolutionary Bioinformatics
• Subjects: Hybridization networks; reticulate evolution; agreement forest
• Online Access: http://la-press.com/article.php?article_id=263

Hybridization is an important evolutionary process for many groups of species. Thus, conflicting signals in a data set may not be the result of sampling or modeling errors, but due to the fact that hybridization has played a significant role in the evolutionary history of the species under consideration. Assuming that the initial set of gene trees is correct, a basic problem for biologists is to compute this minimum number of hybridization events to explain this set. In this paper, we describe a new reduction-based algorithm for computing the minimum number, when the initial data set consists of two trees. Although the two-tree problem is NP-hard, our algorithm always gives the exact solution and runs efficiently on many real biological problems. Previous algorithms for the two-tree problem either solve a restricted version of the problem or give an answer with no guarantee of the closeness to the exact solution. We illustrate our algorithm on a grass data set. This new algorithm is freely available for application at either http://www.bi.uni-duesseldorf.de/~linz or http://www.math.canterbury.ac.nz/~cas83.