HHGtest                 HHG test for association of two distance
                        matrices
MantelTest              Mantel test for association of two distance
                        matirces
RVtest                  RV test for association of two distance
                        matrices
RandIndexTest           Rand Index Test
createHapMat            Create an object of class 'hapMat'
dCorTest                dCor test for similarity of two matrices
ex_hapMatSmall_data     Example small dataset
ex_hapMat_data          Example dataset
perfectphyloR-package   Reconstruct perfect phylogenies from DNA
                        sequence data
phenoDist               Phenotypic distances
plotDend                Plot reconstructed dendrogram
rdistMatrix             Rank-based distances between haplotypes in a
                        given partition
reconstructPP           Reconstruct the perfect phylogeny at a given
                        focal SNV
reconstructPPregion     Reconstruct perfect phylogeny sequencce across
                        a region
tdend                   True dendrogram object
testAssoDist            Test the association between a comparator
                        distance matrix, and the reconstructed
                        dendrograms across a genomic region
testDendAssoRI          Tests Rand Index between a comparator
                        dendrogram and reconstructed dendrograms
vcftohapMat             Create a 'hapMat' object from variant call
                        format ('vcf') file.
