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

Return type

Double[][]