A practical O(n log2n) time algorithm for computing the triplet distance on binary trees

The triplet distance is a distance measure that compares two rooted trees on the same set of leaves by enumerating all sub-sets of three leaves and counting how often the induced topologies of the tree are equal or different. We present an algorithm that computes the triplet distance between two roo...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 14; no. Suppl 2; p. S18
Main Authors: Sand, Andreas, Brodal, Gerth Stølting, Fagerberg, Rolf, Pedersen, Christian NS, Mailund, Thomas
Format: Journal Article
Language:English
Published: London BioMed Central 21.01.2013
Springer Nature B.V
Subjects:
Algorithms
Bioinformatics
Biomedical and Life Sciences
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer science
Computer Simulation
Leaves
Life Sciences
Microarrays
Phylogeny
Proceedings
Software
Studies
Lower Common Ancestor
Brodal
Contractible Edge
Time Algorithm
Binary Tree
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary:The triplet distance is a distance measure that compares two rooted trees on the same set of leaves by enumerating all sub-sets of three leaves and counting how often the induced topologies of the tree are equal or different. We present an algorithm that computes the triplet distance between two rooted binary trees in time O ( n log 2 n ). The algorithm is related to an algorithm for computing the quartet distance between two unrooted binary trees in time O ( n log n ). While the quartet distance algorithm has a very severe overhead in the asymptotic time complexity that makes it impractical compared to O ( n 2 ) time algorithms, we show through experiments that the triplet distance algorithm can be implemented to give a competitive wall-time running time.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-14-S2-S18