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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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/