jebl.evolution.distances

Class TamuraNeiDistanceMatrix

java.lang.Object

jebl.evolution.distances.BasicDistanceMatrix

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

Constructors

Constructor and Description
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