Neighbor Joining As Minimum Evolution
Neighbor joining may be viewed as a greedy algorithm for optimizing a tree according to the 'balanced minimum evolution' (BME) criterion. For each topology, BME defines the tree length (sum of branch lengths) to be a particular weighted sum of the distances in the distance matrix, with the weights depending on the topology. The BME optimal topology is the one which minimizes this tree length. Neighbor joining at each step greedily joins that pair of taxa which will give the greatest decrease in the estimated tree length. This procedure is not guaranteed to find the topology which is optimal by the BME criterion, although it often does and is usually quite close.
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