Package jebl.evolution.distances
Class TamuraNeiDistanceMatrix
- java.lang.Object
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- jebl.evolution.distances.BasicDistanceMatrix
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- jebl.evolution.distances.TamuraNeiDistanceMatrix
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- 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
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Constructor Summary
Constructors Constructor Description TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress)
TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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Method Summary
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Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix
getDistance, getDistance, getDistances, getSize, getSubmatrix, getTaxa
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Constructor Detail
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TamuraNeiDistanceMatrix
public TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) throws CannotBuildDistanceMatrixException
- Throws:
CannotBuildDistanceMatrixException
- only if useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable is false
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TamuraNeiDistanceMatrix
public TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress) throws CannotBuildDistanceMatrixException
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