Package org.biojava.nbio.phylo

Class DistanceTreeEvaluator

java.lang.Object

org.biojava.nbio.phylo.DistanceTreeEvaluator

public class DistanceTreeEvaluator
extends Object

Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.

Author:

Scooter Willis, Aleix Lafita

Method Summary

Modifier and Type	Method	Description
static double	evaluate(org.forester.phylogeny.Phylogeny tree, org.forester.evoinference.matrix.distance.DistanceMatrix matrix)	Evaluate the goodness of fit of a given tree to the original distance matrix.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

evaluate

public static double evaluate(org.forester.phylogeny.Phylogeny tree,
                              org.forester.evoinference.matrix.distance.DistanceMatrix matrix)

Evaluate the goodness of fit of a given tree to the original distance matrix. The returned value is the coefficient of variation, i.e. the square root of the LS error normalized by the mean.

This measure can also give an estimate of the quality of the distance matrix, because a bad fit may mean that the distance is non-additive.

Parameters:

tree - Phylogenetic Distance Tree to evaluate

matrix - Distance Matrix with the original distances

Returns:

the square root of the average tree LS error normalized by the average tree distance (coefficient of variation, CV).