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Issue No.01 - January-February (2011 vol.8)
pp: 2-13
Megan Owen , North Carolina State University, Raleigh
J. Scott Provan , University of North Carolina, Chapel Hill
ABSTRACT
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths is the length of the shortest path between them in the continuous tree space introduced by Billera, Holmes, and Vogtmann. This tree space provides a powerful tool for studying and comparing phylogenetic trees, both in exhibiting a natural distance measure and in providing a euclidean-like structure for solving optimization problems on trees. An important open problem is to find a polynomial time algorithm for finding geodesics in tree space. This paper gives such an algorithm, which starts with a simple initial path and moves through a series of successively shorter paths until the geodesic is attained.
INDEX TERMS
Geometrical problems and computations, trees, graph theory, biology and genetics, phylogenetics, distance.
CITATION
Megan Owen, J. Scott Provan, "A Fast Algorithm for Computing Geodesic Distances in Tree Space", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 1, pp. 2-13, January-February 2011, doi:10.1109/TCBB.2010.3
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