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PhyloFusion- Fast and easy fusion of rooted phylogenetic trees into rooted phylogenetic networks

Zhang, Louxin1; Cetinkaya, Banu2; Huson, Daniel2

Published Jul 10, 2025 on Dryad. https://doi.org/10.5061/dryad.k3j9kd5h5

Data files

Jul 10, 2025 version files 3.54 MB

Abstract

Unrooted phylogenetic networks are commonly used to represent evolutionary data in the presence of incompatibilities. While rooted phylogenetic networks provide a more explicit framework for depicting evolutionary histories involving reticulate events, they remain rarely reported in biological literature, likely due to the lack of widely adopted computational tools.

Here, we introduce PhyloFusion, a fast and user-friendly method for constructing rooted phylogenetic networks from sets of rooted phylogenetic trees. 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 datasets comprising tens of trees and hundreds of taxa.