An algorithm for constructing local regions in a phylogenetic network

Huber, K. T., Watson, E. E. and Hendy, M. D. (2001) An algorithm for constructing local regions in a phylogenetic network. Molecular Phylogenetics and Evolution, 19 (1). pp. 1-8. ISSN 1055-7903

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Abstract

The groupings of taxa in a phylogenetic tree cannot represent all the conflicting signals that usually occur among site patterns in aligned homologous genetic sequences. Hence a tree-building program must compromise by reporting a subset of the patterns, using some discriminatory criterion. Thus, in the worst case, out of possibly a large number of equally good trees, only an arbitrarily chosen tree might be reported by the tree-building program as “The Tree.” This tree might then be used as a basis for phylogenetic conclusions. One strategy to represent conflicting patterns in the data is to construct a network. The Buneman graph is a theoretically very attractive example of such a network. In particular, a characterization for when this network will be a tree is known. Also the Buneman graph contains each of the most parsimonious trees indicated by the data. In this paper we describe a new method for constructing the Buneman graph that can be used for a generalization of Hadamard conjugation to networks. This new method differs from previous methods by allowing us to focus on local regions of the graph without having to first construct the full graph. The construction is illustrated by an example.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Computational Biology
Depositing User:	Vishal Gautam
Date Deposited:	09 Mar 2011 08:20
Last Modified:	16 Jun 2023 23:47
URI:	https://ueaeprints.uea.ac.uk/id/eprint/23800
DOI:	10.1006/mpev.2000.0891

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