Package pal.distance

Class JukesCantorDistanceMatrix

java.lang.Object
pal.distance.DistanceMatrix
pal.distance.JukesCantorDistanceMatrix
All Implemented Interfaces:
Serializable, IdGroup

public class JukesCantorDistanceMatrix extends DistanceMatrix
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:
  • Constructor Details

    • JukesCantorDistanceMatrix

      public JukesCantorDistanceMatrix(DistanceMatrix dist)
      compute jukes-cantor corrected distances (assumes nucleotides as underlying data)
      Parameters:
      dist - distance matrix
    • JukesCantorDistanceMatrix

      public JukesCantorDistanceMatrix(DistanceMatrix dist, int numStates)
      compute jukes-cantor corrected distances
      Parameters:
      dist - distance matrix
      numStates - number of states of underlying data
    • JukesCantorDistanceMatrix

      public JukesCantorDistanceMatrix(Alignment alignment)
      compute jukes-cantor corrected distances
      Parameters:
      alignment - Alignment
    • JukesCantorDistanceMatrix

      public JukesCantorDistanceMatrix(SitePattern sitePattern)
      compute jukes-cantor corrected distances
      Parameters:
      sitePattern - SitePattern