Package pal.distance
Class DistanceTool
java.lang.Object
pal.distance.DistanceTool
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final DistanceMatrix
Construct a distance matrix object such that the distance between sequence A, and sequence B, is the evolutionary distance by a given substitution model.
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Constructor Details
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DistanceTool
public DistanceTool()
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Method Details
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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.
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