distance function
distance(Alignment alignment, String m)
It computes a matrix of pairwise distances from a given alignment using an evolutionary model. If there is a gap or an ambiguous state, it is treated as different from any canonical states.
Parameters
- Alignment alignment - the alignment (no unambiguous states).
- String m - (optional) the evolutionary model, such as JC96 or p, default to p (Hamming) distance