Abstract
We develop and study two distance metrics for area cladograms (leaf-labeled trees where many leaves can share the same label): the edge contract-and-refine metric and the MAAC distance metric. We demonstrate that in contrast to phylogenies, the contract-and-refine distance between two area cladograms is not identical to the character encoding distance, and the latter is not a metric. We present a polynomial time algorithm to compute the MAAC distance, based on a polynomial-time algorithm for computing the largest common pruned subtree of two area cladograms. We also describe a linear time algorithm to decide if two area cladograms are identical.
The research of Ganeshkumar Ganapathy was supported by NSF grants 0331453 and 0121680, Vijaya Ramachandran by NSF CCF-0514876, Tandy Warnow by NSF grants 0331453, 0312830, and 0121680, Barbara Goodson by NSF IGERT training grant 0114387, and Robert Jansen by NSF grant DEB 0120709.
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Ganapathy, G., Goodson, B., Jansen, R., Ramachandran, V., Warnow, T. (2005). Pattern Identification in Biogeography. In: Casadio, R., Myers, G. (eds) Algorithms in Bioinformatics. WABI 2005. Lecture Notes in Computer Science(), vol 3692. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557067_10
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DOI: https://doi.org/10.1007/11557067_10
Publisher Name: Springer, Berlin, Heidelberg
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