IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Pseudo-Line Arrangements: Duality, Algorithms, and Applications
SIAM Journal on Computing
Linearly independent split systems
European Journal of Combinatorics
Improved Layout of Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Graph Theory
Counting Faces in Split Networks
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
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Split networks are commonly used to visualize collections of bipartitions, also called splits, of a finite set. Such collections arise, for example, in evolutionary studies. Split networks can be viewed as a generalization of phylogenetic trees and may be generated using the SplitsTree package. Recently, the NeighborNet method for generating split networks has become rather popular, in part because it is guaranteed to always generate a circular split system, which can always be displayed by a planar split network. Even so, labels must be placed on the "outside” of the network, which might be problematic in some applications. To help circumvent this problem, it can be helpful to consider so-called flat split systems, which can be displayed by planar split networks where labels are allowed on the inside of the network too. Here, we present a new algorithm that is guaranteed to compute a minimal planar split network displaying a flat split system in polynomial time, provided the split system is given in a certain format. We will also briefly discuss two heuristics that could be useful for analyzing phylogeographic data and that allow the computation of flat split systems in this format in polynomial time.