Journal article

A partial order and cluster-similarity metric on rooted phylogenetic trees

Michael Hendriksen, Andrew Francis

JOURNAL OF MATHEMATICAL BIOLOGY | SPRINGER HEIDELBERG | Published : 2020

Abstract

Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in the neighbourhood of each other have similar hierarchies. In the present paper we introduce a new cluster-similarity metric on rooted phylogenetic tree space that has an associated local operation, allowing for easy calculation of neighbourhoods, a trait that is desirable for MCMC calculations. The metric is defined by the distance on the Hasse diagram induced by a partial order on the set of rooted phylogenetic trees, itself based on the notion of a hierar..

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Funding Acknowledgements

The authors thank the reviewers of the manuscript for many valuable suggestions, and Alexei Drummond and Bill Martin for helpful discussions while this manuscript was in preparation, at the New Zealand Phylogenetics meeting in February 2019. The first author thanks Western Sydney University for its support in the form of an Australian Postgraduate Award during this research.