# Reconstruct Perfect Phylogenies from DNA Sequence Data

## Documentation for package ‘perfectphyloR’ version 0.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.