Package pal.distance
Class JukesCantorDistanceMatrix
java.lang.Object
pal.distance.DistanceMatrix
pal.distance.JukesCantorDistanceMatrix
- All Implemented Interfaces:
Serializable
,IdGroup
compute jukes-cantor corrected distance matrix
- Version:
- $Id: JukesCantorDistanceMatrix.java,v 1.5 2002/12/05 04:27:28 matt Exp $
- Author:
- Alexei Drummond, Korbinian Strimmer
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Constructor Summary
ConstructorsConstructorDescriptionJukesCantorDistanceMatrix
(Alignment alignment) compute jukes-cantor corrected distancesJukesCantorDistanceMatrix
(SitePattern sitePattern) compute jukes-cantor corrected distancescompute jukes-cantor corrected distances (assumes nucleotides as underlying data)JukesCantorDistanceMatrix
(DistanceMatrix dist, int numStates) compute jukes-cantor corrected distances -
Method Summary
Methods inherited from class pal.distance.DistanceMatrix
absoluteDistance, addDistance, getClonedDistances, getClosestIndex, getClosestIndex, getDistance, getDistances, getIdCount, getIdentifier, getIdGroup, getSize, isSymmetric, meanDistance, printPHYLIP, setDistance, setDistances, setIdentifier, setIdGroup, squaredDistance, toString, whichIdNumber
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Constructor Details
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JukesCantorDistanceMatrix
compute jukes-cantor corrected distances (assumes nucleotides as underlying data)- Parameters:
dist
- distance matrix
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JukesCantorDistanceMatrix
compute jukes-cantor corrected distances- Parameters:
dist
- distance matrixnumStates
- number of states of underlying data
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JukesCantorDistanceMatrix
compute jukes-cantor corrected distances- Parameters:
alignment
- Alignment
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JukesCantorDistanceMatrix
compute jukes-cantor corrected distances- Parameters:
sitePattern
- SitePattern
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