Maximum Likelihood

Maximum likelihood is the third method used to build trees. Likelihood provides probabilities of the sequences given a model of their evolution on a particular tree. The more probable the sequences given the tree, the more the tree is preferred. All possible trees are considered; computationally intense. Because the user can choose a model of evolution, the method can be useful for widely divergent groups or other difficult situations.

The resultant value is the "probability" (technically, "likelihood") of the observed sequences, assuming a specific model of evolution given this tree. This "probability" is presented as a log likelihood, thus the less negative (or larger) the number, the greater the probability.