pal.distance
Class DistanceTool

java.lang.Object
  pal.distance.DistanceTool

public final class DistanceTool
extends java.lang.Object

Constructor Summary

DistanceTool()

Method Summary

static 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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.