Implementations and Variants
There are many programs available implementing neighbor joining. RapidNJ, QuickJoin and NINJA are fast implementations which run in time in the worst case, but do better on average. BIONJ and Weighbor are variants of neighbor joining which improve on its accuracy by making use of the fact that the shorter distances in the distance matrix are generally better known than the longer distances. FastME is an implementation of the closely related balanced minimum evolution method.
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