perfectphyloR

perfectphyloR is an R package that reconstructs local perfect phylogenies from a sample of binary genetic sequences. A perfect phylogeny is a rooted binary tree that recursively partitions the sequences, providing insights into their ancestral patterns and relationships.

Key features and applications of perfectphyloR include:

1. Reconstructing nested partitions of sequences, which can indicate common ancestral haplotypes.

2. Associating the reconstructed partitions with user-defined partitions allows for customization and specific analyses.

3. Providing insights into the ancestral structure of the sequence data can help understand the samples' evolutionary history.

4. Enabling the mapping of trait-influencing variants by analyzing the reconstructed partitions.