Analogy- This is a term to describe two characters that superficially appear to have descended from a common ancestor.  Analogies are usually easier to identify with morphological data as two analogous characters are not expected to share more than superficial similarities (take for example flight in birds and bats).  It is more difficult to identify analogies in molecular data.

Ancestral Sequence- This is an hypothesized sequence, reconstructed from the relationships between contemporary sequences.  Ancestral sequences can be reconstructed using Maximum Parsimony or Maximum Likelihood.

Autapomorphy- This is a character state that is seen in a single sequence and no other. Sometimes called a uniquely-derived character state.

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