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. 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.
 , The sequence data for Figure 2 was downloaded from Gruenstaeudl, Plant Systematics and Evolution (2019) and then trees were computed using IQ-Tree (Minh et al, 2020). Phylogenetic networks were computed using our implementation of the PhyloFusion method.
Synthetic trees used in Figure 10 and 11 where generated using the SplitsTree app tool 'sample-trees' (Huson & Bryant, 2024).
Data used in Figure 12 is from (Bernardini et al, 2024)., , # PhyloFusion- Fast and easy fusion of rooted phylogenetic trees into rooted phylogenetic networks

[https://doi.org/10.5061/dryad.k3j9kd5h5](https://doi.org/10.5061/dryad.k3j9kd5h5)

## Description of the data and file structure

`Background.zip`: contains a single file \"Background.tre\" that represents the large background tree from which the problem instances used in Figure 10 were generated, in Newick format.

`Figure_2.zip`: For each of the six named gene classes (atp, ndh, pet, psa, psb, photosynthesis), we provide three files:

* name.stree6 - SplitsTree 6 file containing PhyloFusion analysis of gene \"name\"
* name.tre - the input trees for the named gene set
* name.pdf - the PDF showing the network

The directory also contains a SplitsTree 6  file called \"all-iqtree.stree6\" that contains all 78 gene trees computed using IQ-TREE. 

`Figure_10.zip`: Contains two subfolders, \"phylofusion\" and \"fhynch\", each with 12 output files that include input trees and output networks. Files foll...,