Package pal.distance

Class JukesCantorDistanceMatrix

  • All Implemented Interfaces:
    java.io.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:
    Serialized Form
    • Constructor Detail

      • 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