Compatibility is another attempt to define a target function for the phylogeny problem: the number of characters which are compatible with the given tree. We will try finding the phylogeny which is compatible with as many characters as possible.
Note that when we say that a character c has k states, that means that there are k different values of cin the input. For instance, if for a given DNA site all the species in the input have either `T' or `C', this site has only 2 states, and not 4. It is clear then, that a k-state character can have no less than k-1 changes.
In the following discussion, we will assume that all characters are binary, i.e., have exactly two possible states, 0 and 1.
Example 9.7
The binary character presented in the tree in figure
9.1 is compatible with that tree.
