Package pal.distance

Class DistanceTool


  • public final class DistanceTool
    extends java.lang.Object
    • Constructor Detail

      • DistanceTool

        public DistanceTool()
    • Method Detail

      • 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.