TamuraNeiDistanceMatrix (JEBL2 lib API)

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	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

Class TamuraNeiDistanceMatrix

Constructor Summary

Method Summary

Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix

Methods inherited from class java.lang.Object

Constructor Detail

TamuraNeiDistanceMatrix

TamuraNeiDistanceMatrix