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Updated: Jan 1, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
perfectphyloR: An R package for reconstructing perfect phylogenies
Charith B Karunarathna1, Jinko Graham2
1Department of Statistics and Actuarial Science, 8888 University Drive, Burnaby, V5A 1S6, Canada.
Background:
A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype.
Results:
We present an R package perfectphyloR to reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package.
Conclusion:
The perfectphyloR package should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.
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