jebl.evolution.distances
Class TamuraNeiDistanceMatrix

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

public class TamuraNeiDistanceMatrix
extends BasicDistanceMatrix

Date: 22/01/2006 Time: 17:28:59

Version:
$Id: TamuraNeiDistanceMatrix.java 996 2009-03-31 01:15:35Z amyzeta $ Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial DNA in Humans and Chimpanzees. Koichiro Tamura and Masatoshi Nei, 1993 Estimated Distance is d = 2 (pi(A) pi(G) k_R + pi(T) pi(C) k_Y + PI(A)PI(C)) t, where k_R/k_Y are the rates of Purine/Pyrimidine respectivly. When distances grow large, the formulas break as estimates of number of transition/transversion becomes inconsistent, which results in negative logs. Returning "infinity" is not optimal as it breaks operations such as constructing consensus trees where distances for resampled sequences vary between (say) 2-3 and out "infinity" 10. As a workaround I try to reduce the number of transitions/transversions by the minimum amout which brings the estimates back to a consistent state.
Author:
Joseph Heled

Constructor Summary
TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress)
           
TamuraNeiDistanceMatrix(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

TamuraNeiDistanceMatrix

public TamuraNeiDistanceMatrix(Alignment alignment,
                               ProgressListener progress,
                               boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
                        throws CannotBuildDistanceMatrixException
Throws:
CannotBuildDistanceMatrixException - only if useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable is false

TamuraNeiDistanceMatrix

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


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