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Neighbor-Joining Revealed Olivier Gascuel* and Mike Steel

Summary: REVIEW
Neighbor-Joining Revealed
Olivier Gascuel* and Mike Steel
*LIRMM, Montpellier, France and Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
It is nearly 20 years since the landmark paper (Saitou and Nei 1987) in Molecular Biology and Evolution introducing
Neighbor-Joining (NJ). The method has become the most widely used method for building phylogenetic trees from dis-
tances, and the original paper has been cited about 13,000 times (Science Citation Index). Yet the question ``what does the
NJ method seek to do?'' has until recently proved somewhat elusive, leading to some imprecise claims and misunder-
standing. However, a rigorous answer to this question has recently been provided by further mathematical investigation,
and the purpose of this note is to highlight these results and their significance for interpreting NJ. The origins of this story lie
in a paper by Pauplin (2000) though its continuation has unfolded in more mathematically inclined literature. Our aim here
is to make these findings more widely accessible.
First we review briefly the Neighbor-Joining (NJ)
method and outline what it does ``not'' do. NJ builds a tree
from a matrix of pairwise evolutionary distances relating
the set of taxa being studied. The distance between any
taxon pair i and j is denoted as d(i, j) and can be obtained
from sequence data by a variety of approaches, for example,
using Kimura's (1980) 2-parameter estimate. NJ iteratively
selects a taxon pair, builds a new subtree, and agglomerates


Source: Anisimova, Maria - Institute of Scientific Computing, Eidgenössische Technische Hochschule Zürich (ETHZ)
Sullivan, Jack - Department of Biological Sciences, University of Idaho


Collections: Biology and Medicine; Environmental Sciences and Ecology