Computing Phylogenetic Diversity for Split Systems

Spillner, Andreas, Nguyen, Binh T. and Moulton, Vincent (2008) Computing Phylogenetic Diversity for Split Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5 (2). pp. 235-244. ISSN 1545-5963

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Abstract

In conservation biology, it is a central problem to measure, predict, and preserve biodiversity as species face extinction. In 1992, Faith proposed measuring the diversity of a collection of species in terms of their relationships on a phylogenetic tree and using this information to identify collections of species with high diversity. Here, we are interested in some variants of the resulting optimization problem that arise when considering species whose evolution is better represented by a network rather than a tree. More specifically, we consider the problem of computing phylogenetic diversity relative to a split system on a collection of species of size n. We show that, for general split systems, this problem is NP-hard. In addition, we provide some efficient algorithms for some special classes of split systems, in particular presenting an optimal O(n) time algorithm for phylogenetic trees and an O(n log n + nk) time algorithm for choosing an optimal subset of size k relative to a circular split system.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Related URLs:
Depositing User: Vishal Gautam
Date Deposited: 07 Mar 2011 13:36
Last Modified: 21 Apr 2020 19:07
URI: https://ueaeprints.uea.ac.uk/id/eprint/23128
DOI: 10.1109/TCBB.2007.70260

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