Method Detail

• evaluate

  public static double evaluate(Phylogeny tree,
                                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).