Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric

The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the first in a series of papers devoted to the analysis and comparison of metrics for tree-child time-consistent phylogenetic networks on the same set of taxa. In this paper,...

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Bibliographic Details
Published in:IEEE/ACM transactions on computational biology and bioinformatics 2009-01, Vol.6 (1), p.46-61
Main Authors: Cardona, G., Llabres, M., Rossello, F., Valiente, G.
Format: Article
Language:English
Subjects:
Algorithms
Biology and genetics
Computational Biology - methods
DNA
Evolution (biology)
Evolution, Molecular
Gene Transfer, Horizontal
Genetics
Graph algorithms
History
Hybridization, Genetic
Mathematics
Models, Genetic
Organisms
Phylogeny
Recombination, Genetic
Reconstruction algorithms
Sequences
Time Factors
Tree graphs
Trees
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Summary:The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the first in a series of papers devoted to the analysis and comparison of metrics for tree-child time-consistent phylogenetic networks on the same set of taxa. In this paper, we study three metrics that have already been introduced in the literature: the Robinson-Foulds distance, the tripartition distance, and the mu-distance. They generalize to networks the classical Robinson-Foulds or partition distance for phylogenetic trees. We analyze the behavior of these metrics by studying their least and largest values and when they achieve them. As a by-product of this study, we obtain tight bounds on the size of a tree-child time-consistent phylogenetic network.
ISSN:1545-5963
1557-9964
DOI:10.1109/TCBB.2008.70