Neighbor joining

From Palaeos

Neighbour joining is a method of phylogenetic analysis using a set of aligned DNA or protein sequences that calculates the amount of differences between taxa and constructs a tree with more similar taxa closer together. The root of the tree generally lies between the most dissimilar taxa. Because neighbour joining only considers the overall differences/similarities, and does not consider the nature of the differences or distinguish between ancestral and derived characters, it should be regarded as a phenetic method.

Neighbour joining has mostly fallen out of favour as a method, for the same reasons as other phenetic methods - it is very vulnerable to variation in evolutionary rates, biases in mutations, etc. As such, it has been replaced by methods such as maximum parsimony or maximum likelihood (an exception is in prokaryote phylogenetics, where for some reason neighbour joining remains very popular). Neighbour joining's one advantage is that the calculations involved are exceedingly simple, and it may still be used where processing time is at a premium, or to give a rough preliminary guide to what the final result may look like.

Credits

CKT061212