A satisfiability-based approach for embedding generalized tanglegrams on level graphs

Authors:
Ewald Speckenmeyer;Andreas Wotzlaw;Stefan Porschen
Affiliations:
Institut für Informatik, Universität zu Köln, Köln, Germany;Institut für Informatik, Universität zu Köln, Köln, Germany;Fachbereich, HTW-Berlin, Treskowallee, Berlin, Germany
Venue:
SAT'11 Proceedings of the 14th international conference on Theory and application of satisfiability testing
Year:
2011

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Abstract

A tanglegram is a pair of trees on the same set of leaves with matching leaves in the two trees joined by an edge. Tanglegrams are widely used in computational biology to compare evolutionary histories of species. In this paper we present a formulation of two related combinatorial embedding problems concerning tanglegrams in terms of CNF-formulas. The first problem is known as planar embedding and the second as crossing minimization problem. We show that our satisfiability formulation of these problems can handle a much more general case with more than two, not necessarily binary or complete, trees defined on arbitrary sets of leaves and allowed to vary their layouts.