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Related Concept Videos

Phylogenetic Trees03:21

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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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A Practical Guide to Phylogenetics for Nonexperts
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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.

BMC Bioinformatics
|December 25, 2019
PubMed
Summary
This summary is machine-generated.

Researchers can now reconstruct ancestral relationships in genetic data using the perfectphyloR R package. This tool helps identify common ancestral haplotypes and map trait-influencing variants for deeper biological insights.

Keywords:
AncestryPerfect phylogenySequenceTrait-influencing variants

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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.