| perfectphyloR-package | Reconstruct perfect phylogenies from DNA sequence data |
| 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 |
| HHGtest | HHG test for association of two distance matrices |
| MantelTest | Mantel test for association of two distance matirces |
| perfectphyloR | Reconstruct perfect phylogenies from DNA sequence data |
| phenoDist | Phenotypic distances |
| plotDend | Plot reconstructed dendrogram |
| RandIndexTest | Rand Index Test |
| 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 |
| RVtest | RV test for association of two distance matrices |
| 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. |