Distance based

The distance based methods that we will go over here include UPGMA (unweighted pair group method with arithmetic mean) and neighbor joining. Both of these methods are exact in that they don’t require search tree space and instead they construct a single tree by joining nodes that are the closest in distance.

UPGMA

UPGMA is a method that produces a rooted tree and assumes that the evolution is clock like (i.e., doesn’t allow for rates to differ between species). The constant rate assumption is generally a bad assumption and is violated by most data. Nevertheless, it provides a good demonstration of how distance methods are used and will provide the motivation for the development of the neighbor joining method which doesn’t suffer from this same problem.

Neighbor joining

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