perfectphyloR: An R package for reconstructing perfect phylogenies

Area of Science:

• Computational Biology
• Bioinformatics
• Genetics

Background:

• A perfect phylogeny is a rooted binary tree model used to represent the evolutionary history of genetic sequences.
• Nested partitions within a perfect phylogeny reveal patterns of ancestry and common ancestral haplotypes.
• Understanding sequence ancestry is crucial for genetic research and variant analysis.

Purpose of the Study:

• To introduce the perfectphyloR R package for reconstructing local perfect phylogenies.
• To enable users to associate reconstructed partitions with their own defined partitions.
• To demonstrate the core functionalities of the perfectphyloR package.

Main Methods:

• Development of an R package named perfectphyloR.
• Implementation of algorithms for reconstructing perfect phylogenies from binary sequence data.
• Tools for associating reconstructed phylogenetic partitions with user-defined groupings.

Main Results:

• The perfectphyloR package successfully reconstructs local perfect phylogenies.
• The package allows for the association of reconstructed partitions with user-defined structures.
• Demonstration of the package's major functionalities is provided.

Conclusions:

• The perfectphyloR package offers valuable tools for researchers analyzing sequence data ancestry.
• Reconstructed partitions can be applied to various biological questions, including mapping trait-influencing variants.
• This package enhances the ability to gain insights into the ancestral structure of genetic data.