Zhang, L.; Cetinkaya, B.; Huson, D.

Unrooted phylogenetic networks are often used to represent evolutionary data when incompatibilities are present. Although rooted phylogenetic networks are better suited for explicitly depicting evolutionary histories that involve reticulate events, they have been rarely used in practice, due to a lack of appropriate methods for their calculation. Here we present PhyloFusion, a fast and easily-applicable method for calculating rooted phylogenetic networks on sets of rooted phylogenetic trees. The algorithm can handle trees with unresolved nodes (which arise when edges with low support are contracted) and missing taxa. We illustrate how to use the algorithm to explore different groups of functionally-related genes and report that the algorithm can be applied to datasets containing tens of trees and hundreds of taxa.