A perfect phylogeny is a rooted binary tree that recursively partitions DNA sequences according to their ancestry. We present our progress on an R package perfectphyloR which reconstructs the local perfect phylogenies underlying a sample of sequences. We first partition the sequences using the algorithm of Gusfield and then further partition them using heuristics introduced by Mailund. The reconstructed perfect phylogenies for a sample of sequences can provide insight into their patterns of ancestry. For example, disease sequences may cluster together on a local ancestral tree indicating that they arise from a common ancestral mutation. The perfectphyloR package should therefore be useful to researchers seeking the ancestral structure of their sequence data in order to associate it with disease phenotypes. We will present examples of useful functions that we are developing for the package to explore the sequence data and associate its ancestry to phenotypes.