View source for Neighbour joining

In [[:Category:Bioinformatics|bioinformatics]], '''neighbour-joining''' is a bottom-up clustering method used for the creation of [[phylogeny|phylogenetic]] [[tree data structure|tree]]s. Usually used for trees based on [[DNA]] or [[protein]] [[primary structure|sequence]] data, the algorithm requires knowledge of the distance between each pair of taxa (e.g. species or sequences) in the tree.  

Neighbour-joining is based on the minimum evolution criterion for [[phylogenetic tree]]s, i.e. the topology that gives the least total branch length is preferred at each step of the algorithm. However, neighbour-joining may not find the true tree topology with least total branch length because it is a greedy algorithm that constructs the tree in a step-wise fashion.  Even though it is sub-optimal in this sense, it has been extensively tested and usually finds a tree that is quite close to the optimal tree.  

The main virtue of neighbour-joining is its efficiency. It can be used on very large data sets for which other means of phylogenetic analysis (e.g. [[minimum evolution]], [[maximum parsimony]], [[maximum likelihood]]) are computationally prohibitive. Unlike the [[UPGMA]] algorithm for phylogenetic tree reconstruction, neighbour-joining does not assume that all lineages evolve at the same rate ([[molecular clock hypothesis]]) and produces an unrooted tree.

==References==
*Saitou N, Nei M (1987). "The neighbor-joining method: a new method for reconstructing phylogenetic trees". ''Mol Biol Evol, 4(4):406-425''.

==External links==
*[http://en.wikipedia.org/wiki/Neighbour_joining Wikipedia article on '''Neighbour joining''']

{{Phylogenetics}}
[[Category:Phylogenetics]]