CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010 vol.7 Issue No.04 - October-December

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Issue No.04 - October-December (2010 vol.7)

pp: 588-597

Balaji Venkatachalam , University of California Davis, Davis

Jim Apple , University of California Davis, Davis

Katherine St. John , Lehman College and City University of New York, New York

Dan Gusfield , University of California Davis, Davis

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.57

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 biology—to compare evolutionary histories of host and parasite species and to analyze genes of species in the same geographical area. We consider optimization problems in tanglegram drawings. We show a linear time algorithm to decide if a tanglegram admits a planar embedding by a reduction to the planar graph drawing problem. This problem was also studied by Fernau et al. [15]. A similar reduction to a graph crossing problem also helps to solve an open problem they posed, showing a fixed-parameter tractable algorithm for minimizing the number of crossings over all d-ary trees. For the case where one tree is fixed, we show an O(n {\log} n) algorithm to determine the drawing of the second tree that minimizes the number of crossings. This improves the bound from earlier methods. We introduce a new optimization criterion using Spearman's footrule distance and give an O(n^2) algorithm. We also show integer programming formulations to quickly obtain tanglegram drawings that minimize the two optimization measures discussed. We prove lower bounds on the maximum gap between the optimal solution and the heuristic of Dwyer and Schreiber [13] to minimize crossings.

INDEX TERMS

Optimization, combinatorial algorithms, graph algorithms, trees, analysis of algorithms, phylogeny, tree comparison, graph drawing, combinatorics.

CITATION

Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield, "Untangling Tanglegrams: Comparing Trees by Their Drawings",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol.7, no. 4, pp. 588-597, October-December 2010, doi:10.1109/TCBB.2010.57REFERENCES