A sub-cubic time algorithm for computing the quartet distance between two general trees

Jesper Nielsen, Anders Kabell Kristensen, Thomas Mailund, Christian Nørgaard Storm Pedersen

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Abstract

Background
When inferring phylogenetic trees different algorithms may give different trees. To study such effects a measure for the distance between two trees is useful. Quartet distance is one such measure, and is the number of quartet topologies that differ between two trees.

Results
We have derived a new algorithm for computing the quartet distance between a pair of general trees, i.e. trees where inner nodes can have any degree ≥ 3. The time and space complexity of our algorithm is sub-cubic in the number of leaves and does not depend on the degree of the inner nodes. This makes it the fastest algorithm so far for computing the quartet distance between general trees independent of the degree of the inner nodes.

Conclusions
We have implemented our algorithm and two of the best competitors. Our new algorithm is significantly faster than the competition and seems to run in close to quadratic time in practice.
OriginalsprogEngelsk
TidsskriftAlgorithms for Molecular Biology
Vol/bind6
Nummer15
ISSN1748-7188
DOI
StatusUdgivet - 3 jun. 2011

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