Professor Magnus Bordewich m.j.r.bordewich@durham.ac.uk
Professor
A Reduction Algorithm for Computing the Hybridization Number of Two Trees
Bordewich, M.; Linz, S.; St. John, K.; Semple, C.
Authors
S. Linz
K. St. John
C. Semple
Abstract
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.
Citation
Bordewich, M., Linz, S., St. John, K., & Semple, C. (2007). A Reduction Algorithm for Computing the Hybridization Number of Two Trees. Evolutionary Bioinformatics, 3, 86-98
| Journal Article Type | Article |
|---|---|
| Publication Date | May 1, 2007 |
| Deposit Date | Jan 5, 2010 |
| Publicly Available Date | Jan 6, 2010 |
| Journal | Evolutionary Bioinformatics |
| Publisher | SAGE Publications |
| Peer Reviewed | Peer Reviewed |
| Volume | 3 |
| Pages | 86-98 |
| Keywords | Hybridization networks, Reticulate evolution, Agreement forest. |
| Publisher URL | http://www.la-press.com/journal.php?journal_id=17&issue_id=18 |
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Copyright Statement
This work is licensed under a Creative Commons Attribution 3.0 License (http://creativecommons.org/licenses/by/3.0/).
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