Neighbour joining - Revision history

Christoph at 10:35, 19 April 2007

2007-04-19T10:35:51Z

Christoph at 04:53, 13 September 2006

2006-09-13T04:53:40Z

Christoph at 04:48, 13 September 2006

2006-09-13T04:48:47Z

Christoph: Added "References"

2006-01-03T18:34:09Z

Added "References"

Christoph: Started article

2005-12-30T01:19:54Z

Started article

New page

In [[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.

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

[[Category:Academic Research]]
[[Category:Phylogenetics]]

@@ Line 1: / Line 1: @@
-In [[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.
+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.
@@ Line 5: / Line 5: @@
 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 ==
+==References==
-* Saitou N and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. ''Mol Biol Evol'' '''4(4)''':406-425.
+*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 ==
+==External links==
-* [http://en.wikipedia.org/wiki/Neighbour_joining Wikipedia article on '''Neighbour joining''']
+*[http://en.wikipedia.org/wiki/Neighbour_joining Wikipedia article on '''Neighbour joining''']
 {{Phylogenetics}}
 [[Category:Phylogenetics]]

← Older revision		Revision as of 04:53, 13 September 2006
Line 12:		Line 12:

	{{Phylogenetics}}		{{Phylogenetics}}
−	~~[[Category:Academic Research]]~~
	[[Category:Phylogenetics]]		[[Category:Phylogenetics]]

← Older revision		Revision as of 18:34, 3 January 2006
Line 4:		Line 4:

	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.		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 and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. ''Mol Biol Evol'' '''4(4)''':406-425.

	== External links ==		== External links ==