What is "neighbor-net"

NeighborNet 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 split network. If the distance matrix satisfies the Kalmanson combinatorial conditions then Neighbor-net will return the corresponding circular ordering. The method is implemented in the SplitsTree package.

Examples of the application of Neighbor-net can be found in virologyJ. Schmidt-Chanasit, A. Bialonski, P. Heinemann, R. Ulrich, S. Gunther,

H. Rabenau, and H. Doerr. A10-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 -- 237, 2009.

, horticulture, dinosaur genetics, comparative linguistics, and archaeology.