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java.lang.Objectpal.distance.DistanceTool
public final class DistanceTool
Constructor Summary | |
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DistanceTool()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DistanceTool()
Method Detail |
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public static final DistanceMatrix constructEvolutionaryDistances(Alignment a, SubstitutionModel sm)
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.
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