Computing steiner minimum trees in Hamming metric

Authors:
Ernst Althaus;Rouven Naujoks
Affiliations:
Université Henri Poincaré, Vandœuvre-lès-Nancy, France;Max-Planck-Institut für Informatik, Saarbrücken, Germany
Venue:
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
Year:
2006

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Abstract

Computing Steiner minimum trees in Hamming metric is a well studied problem that has applications in several fields of science such as computational linguistics and computational biology. Among all methods for finding such trees, algorithms using variations of a branch and bound method developed by Penny and Hendy have been the fastest for more than 20 years. In this paper we describe a new pruning approach that is superior to previous methods and its implementation.