A perfect phylogeny is a rooted binary tree that recursively partitions DNA sequences. The nested partition structures of a perfect phylogeny provide insight into the pattern of ancestry of DNA sequence data. For example, disease sequences may cluster together in a local partition indicating that they arise from a common ancestral haplotype. The availability of an R package that reconstructs perfect phylogenies should therefore be useful to researchers seeking insight into the ancestral structure of their sequence data. 

We develop an R package perfectphyloR to reconstruct the local perfect phylogenies underlying a sample of DNA sequences. Our implementation first partitions the DNA sequences using a classic partitioning algorithm and then uses well known heuristics to refine them further. We here briefly demonstrate the reconstruction process and illustrate the major functionality of the package using worked examples.