MiS Preprint Repository

We have decided to discontinue the publication of preprints on our preprint server as of 1 March 2024. The publication culture within mathematics has changed so much due to the rise of repositories such as ArXiV ( that we are encouraging all institute members to make their preprints available there. An institute's repository in its previous form is, therefore, unnecessary. The preprints published to date will remain available here, but we will not add any new preprints here.

MiS Preprint

Detecting Phylogenetic Footprint Clusters by Optimizing Barbeques

Axel Mosig, Türker Biyikoglu, Sonja J. Prohaska and Peter F. Stadler


Taking a geometric view on a problem occurring in the context of phylogenetic footprinting, we study the so-called Best Barbeque Problem. The Best Barbeque Problem asks for simultaneously stabbing a maximum number of differently colored intervals from $K$ arrangements of colored intervals. This geometric problem leads to a combinatorial optimization problem, a decision version of which is shown to be NP-complete. Due to its relevance in biological applications, we propose two branch-and-bound algorithms to detect footprint clusters in some real world instances of phylogenetic footprints. Finally, we point out other geometric and combinatorial scenarios where optimizing barbeques might be of practical relevance.

phylogenetic footprint clusters, np-complete, best barbeque problem

Related publications

2005 Repository Open Access
Türker Biyikoglu, Peter F. Stadler, Sonja J. Prohaska and Axel Mosig

Detecting phylogenetic footprint clusters by optimizing barbeques