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To test the fit between data and more than one alternative tree, you can just do a bootstrap analysis, and map the results on a neighbour-net splits graph based on the same data.

Note that the phangorn library includes functions to transfer information between trees/tree samples and trees and networks:<br/> Schliep K, Potts AJ, Morrison DA, Grimm GW. 2017. Intertwining phylogenetic trees and networks. Methods in Ecology and Evolution (DOI:10.1111/2041-210X.12760.)[http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12760/full] – the basic functions and script templates are provided in the associated vignette.