jebl.evolution.distances
Class JukesCantorDistanceMatrix

java.lang.Object
  extended by jebl.evolution.distances.BasicDistanceMatrix
      extended by jebl.evolution.distances.JukesCantorDistanceMatrix
All Implemented Interfaces:
DistanceMatrix

public class JukesCantorDistanceMatrix
extends BasicDistanceMatrix

Compute jukes-cantor corrected distance matrix for a set of aligned sequences. Adapted from BEAST code by joseph.

Version:
$Id: JukesCantorDistanceMatrix.java 998 2009-04-09 03:06:19Z richardmoir $
Author:
Andrew Rambaut, Korbinian Strimmer, Joseph Heled

Constructor Summary
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress)
           
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
           
 
Method Summary
 
Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix
getDistance, getDistance, getDistances, getSize, getSubmatrix, getTaxa
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(Alignment alignment,
                                 ProgressListener progress)
                          throws CannotBuildDistanceMatrixException
Throws:
CannotBuildDistanceMatrixException

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(Alignment alignment,
                                 ProgressListener progress,
                                 boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
                          throws CannotBuildDistanceMatrixException
Throws:
CannotBuildDistanceMatrixException


http://code.google.com/p/jebl2/