Weighted Characters

It is possible to assign weights not only to state changes, but also to the characters themselves. Technically, this means assigning a number W_c to each character, and rewriting equation 9.5 to read:

$$S(T) = \sum_{c=1}^{m}W_c\cdot\min_iS_i(r)$$ (9.5)

Where do we get the weights W_c? For instance, if we are working with a DNA sequence, and we know the reading frame, we can make use of the fact that changes in the third codon position are more frequent, since in many cases they don't change the amino acid coded. In section 9.3 we will see another possible source for weights - compatible characters. In short, we will give more weight to characters which seem to fit the tree well than to characters which fit it poorly.