PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks

Unrooted phylogenetic networks are commonly used to represent evolutionary data in the presence of incompatibilities. Although rooted phylogenetic networks offer a more explicit framework for depicting evolutionary histories involving reticulate events, they are reported less frequently, probably due to a lack of tools that are as easily applicable as those for unrooted networks. Here, we introduce PhyloFusion, a fast and user-friendly method for constructing rooted phylogenetic networks from sets of rooted phylogenetic trees. The resulting networks have the tree-child property. The algorithm accommodates trees with unresolved nodes—often resulting from the contraction of low-support edges—as well as some degree of missing taxa. We demonstrate its application to the analysis of functionally related gene groups and show that it can efficiently handle data sets comprising tens of trees or hundreds of taxa. An open source implementation of PhyloFusion is available as part of the SplitsTree app: https://www.github.com/husonlab/splitstree6. All data available here: https://doi.org/10.5061/dryad.k3j9kd5h5