NeighborNet[1] is an algorithm for constructing phylogenetic networks which is loosely based on the neighbor joining algorithm. Like neighbor joining, the method takes a distance matrix as input, and works by agglomerating clusters. However, the NeighborNet algorithm can lead to collections of clusters which overlap and do not form a hierarchy, and are represented using a type of phylogenetic network called a splits graph. If the distance matrix satisfies the Kalmanson combinatorial conditions then Neighbor-net will return the corresponding circular ordering.[2][3] The method is implemented in the SplitsTree and R/Phangorn[4][5] packages.
Examples of the application of Neighbor-net can be found in virology,[6] horticulture,[7] dinosaur genetics,[8]comparative linguistics,[9] and archaeology.[10]
^Schmidt-Chanasit J, Bialonski A, Heinemann P, Ulrich RG, Günther S, Rabenau HF, Doerr HW (March 2009). "A 10-year molecular survey of herpes simplex virus type 1 in Germany demonstrates a stable and high prevalence of genotypes A and B". Journal of Clinical Virology. 44 (3): 235–7. doi:10.1016/j.jcv.2008.12.016. PMID19186100.