constructEvolutionaryDistances
public static final DistanceMatrix constructEvolutionaryDistances(Alignment a,
SubstitutionModel sm)
Construct a distance matrix object such that the distance between sequence A, and sequence B, is the
evolutionary distance by a given substitution model. The evolutionary distance is the branch length on the
maximum likelihood tree consisting of only sequences A and B at the tips and under the given model
of substitution.
- Parameters:
a
- The aligned set of sequences. The resulting distance matrix has defines a distance between each and every sequence in the input alignment to every other sequence.sm
- The model under which the maximum likelihood calculation is done. The model is not optimised.
- Returns:
- The relating distance matrix of evolutionary distances.