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Subdominant Matroid Ultrametrics
Federico Ardila
Mathematical Sciences Research Institute, 17 Gauss Way, Berkeley, CA 94720-5070, USA
federico@microsoft.com
Annals of Combinatorics 8 (4) p.379-389 December, 2004
AMS Subject Classification: 05B35, 51F99, 92B10
Abstract:
Given a matroid M on the ground set E, the Bergman fan , or space of M-ultrametrics, is a polyhedral complex in which arises in several different areas, such as tropical algebraic geometry, dynamical systems, and phylogenetics. Motivated by the phylogenetic situation, we study the following problem: Given a point w in , we wish to find an M-ultrametric which is closest to it in the
    The solution to this problem follows easily from the existence of the subdominant M-ultrametric: a componentwise maximum M-ultrametric which is componentwise smaller than w. A procedure for computing it is given, which brings together the points of view of matroid theory and tropical geometry.
    When the matroid in question is the graphical matroid of the complete graph Kn, the Bergman fan parameterizes the equidistant phylogenetic trees with n leaves. In this case, our results provide a conceptual explanation for Chepoi and Fichet's method for computing the tree that most closely matches measured data.
Keywords: phylogenetic trees, tropical geometry, Bergman complex, ultrametric

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