Package pal.distance

Class DistanceTool

java.lang.Object
pal.distance.DistanceTool

public final class DistanceTool extends Object
  • Constructor Details

    • DistanceTool

      public DistanceTool()
  • Method Details

    • 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.