perfectphyloR

perfectphyloR reconstructs perfect phylogenies from DNA sequence data by recursively partitioning sequences based on single-nucleotide variants (SNVs) into rooted binary trees that represent ancestral relationships.

Key Features:

• Reconstruction of Perfect Phylogenies: Reconstructs local perfect phylogenies underlying samples of DNA sequences at specified SNVs, producing rooted binary trees of nested partitions.
• Insight into Ancestral Structures: Identifies clusters of sequences that share common ancestral haplotypes within the nested partitioning.
• User-Defined Partition Association: Allows association of reconstructed partitions with user-defined categories.
• Application in Trait Mapping: Enables mapping of trait-influencing variants by relating reconstructed partitions to phenotypic traits or disease susceptibility.

Scientific Applications:

• Genetic Epidemiology: Trace origins and spread of diseases by identifying clusters of pathogenic sequences that share common ancestors.
• Evolutionary Biology: Reconstruct evolutionary histories and divergence patterns among species or populations.
• Genomic Studies: Map trait-influencing variants to identify genetic factors associated with specific traits or conditions.

Methodology:

Reconstruction of local perfect phylogenies from binary sequence data using recursive partitioning to create nested structures that reflect ancestry and evolutionary relationships, with support for integration of user-defined partitions.