, Volume 2, Issue 1, pp 728
First online:
Optimal algorithms for comparing trees with labeled leaves
 William H. E. DayAffiliated withDepartment of Computer Science, Memorial University of Newfoundland
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LetR _{ n } denote the set of rooted trees withn leaves in which: the leaves are labeled by the integers in {1, ...,n}; and among interior vertices only the root may have degree two. Associated with each interior vertexv in such a tree is the subset, orcluster, of leaf labels in the subtree rooted atv. Cluster {1, ...,n} is calledtrivial. Clusters are used in quantitative measures of similarity, dissimilarity and consensus among trees. For anyk trees inR _{ n }, thestrict consensus tree C(T _{1}, ...,T _{ k }) is that tree inR _{ n } containing exactly those clusters common to every one of thek trees. Similarity between treesT _{1} andT _{2} inR _{ n } is measured by the numberS(T _{1},T _{2}) of nontrivial clusters in bothT _{1} andT _{2}; dissimilarity, by the numberD(T _{1},T _{2}) of clusters inT _{1} orT _{2} but not in both. Algorithms are known to computeC(T _{1}, ...,T _{ k }) inO(kn ^{2}) time, andS(T _{1},T _{2}) andD(T _{1},T _{2}) inO(n ^{2}) time. I propose a special representation of the clusters of any treeT R _{ n }, one that permits testing in constant time whether a given cluster exists inT. I describe algorithms that exploit this representation to computeC(T _{1}, ...,T _{ k }) inO(kn) time, andS(T _{1},T _{2}) andD(T _{1},T _{2}) inO(_{n}) time. These algorithms are optimal in a technical sense. They enable wellknown indices of consensus between two trees to be computed inO(n) time. All these results apply as well to comparable problems involving unrooted trees with labeled leaves.
Keywords
Algorithm complexity Algorithm design Comparing hierarchical classifications Comparing phylogenetic trees Consensus index Strict consensus tree Title
 Optimal algorithms for comparing trees with labeled leaves
 Journal

Journal of Classification
Volume 2, Issue 1 , pp 728
 Cover Date
 198512
 DOI
 10.1007/BF01908061
 Print ISSN
 01764268
 Online ISSN
 14321343
 Publisher
 SpringerVerlag
 Additional Links
 Topics
 Keywords

 Algorithm complexity
 Algorithm design
 Comparing hierarchical classifications
 Comparing phylogenetic trees
 Consensus index
 Strict consensus tree
 Industry Sectors
 Authors

 William H. E. Day ^{(1)}
 Author Affiliations

 1. Department of Computer Science, Memorial University of Newfoundland, A1C 5S7, St. John's, Newfoundland, Canada