Counting and enumerating galled networks

Beyond Galled Trees - Decomposition and Computation of Galled Networks

Counting and enumerating aggregate classifiers

We propose a generic model for the “weighted voting” aggregation step performed by several methods in supervised classification. Further, we construct an algorithm to enumerate the number of distinct aggregate classifiers that arise in this model. When there are only two classes in the classification problem, we show that a class of functions that arises from aggregate classifiers coincides wit...

A metric for galled networks

Galled networks, directed acyclic graphs that model evolutionary histories with reticulation cycles containing only tree nodes, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their reconstruction. In this paper we prove that Nakhleh’s m measure is a metric for this class of phylogenetic networks and hence it can be safely u...

Enumerating and Counting Cycles in Bipartite Graphs

Computing galled networks from real data

MOTIVATION Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although promising approaches exist, there are no tools available that biologists could easily and routinely use to compute rooted phylogenetic networks on real datasets containing tens or hundreds o...