A parsimony-based metric for phylogenetic trees

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) A parsimony-based metric for phylogenetic trees. Advances in Applied Mathematics, 66. 22–45. ISSN 0196-8858

Preview

PDF (Tree-Metric) - Draft Version Download (401kB) | Preview

Abstract

In evolutionary biology various metrics have been defined and studied for comparing phylogenetic trees. Such metrics are used, for example, to compare competing evolutionary hypotheses or to help organize algorithms that search for optimal trees. Here we introduce a new metric dpdp on the collection of binary phylogenetic trees each labeled by the same set of species. The metric is based on the so-called parsimony score, an important concept in phylogenetics that is commonly used to construct phylogenetic trees. Our main results include a characterization of the unit neighborhood of a tree in the dpdp metric, and an explicit formula for its diameter, that is, a formula for the maximum possible value of dpdp over all possible pairs of trees labeled by the same set of species. We also show that dpdp is closely related to the well-known tree bisection and reconnection (tbr) and subtree prune and regraft (spr) distances, a connection which will hopefully provide a useful new approach to understanding properties of these and related metrics.

Item Type:	Article
Uncontrolled Keywords:	metric,phylogenetic trees,parsimony score,tree operations,unit neighborhood,diameter
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Data Science and AI
Depositing User:	Pure Connector
Date Deposited:	23 Jul 2015 15:38
Last Modified:	10 Dec 2024 01:25
URI:	https://ueaeprints.uea.ac.uk/id/eprint/53492
DOI:	10.1016/j.aam.2015.02.002

Downloads

Actions (login required)

View Item