NeighborNet is an algorithm for constructing

phylogenetic network A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridi ...

s which is loosely based on the

neighbor joining In bioinformatics, neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic trees, created by Naruya Saitou and Masatoshi Nei in 1987. Usually based on DNA or protein sequence data, the algorithm require ...

algorithm. Like neighbor joining, the method takes a

distance matrix In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set. Depending upon the application involved, the ''dist ...

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 A hierarchy (from Greek: , from , 'president of sacred rites') is an arrangement of items (objects, names, values, categories, etc.) that are represented as being "above", "below", or "at the same level as" one another. Hierarchy is an important ...

, and are represented using a type of phylogenetic network called a splits graph. If the distance matrix satisfies the

Kalmanson combinatorial conditions In mathematics, the Kalmanson combinatorial conditions are a set of conditions on the distance matrix used in determining the solvability of the traveling salesman problem. These conditions apply to a special kind of cost matrix In production, ...

then Neighbor-net will return the corresponding circular ordering. The method is implemented in the

SplitsTree SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. SplitsTree impleme ...

and R/Phangorn packages. Examples of the application of Neighbor-net can be found in virology, horticulture, dinosaur genetics,

comparative linguistics Comparative linguistics, or comparative-historical linguistics (formerly comparative philology) is a branch of historical linguistics that is concerned with comparing languages to establish their historical relatedness. Genetic relatedness ...

, and archaeology.

References

Computational phylogenetics Genetics software Molecular biology {{bioinformatics-stub