perfectphyloR: An R Package For Reconstructing Perfect Phylogenies

Peer reviewed: 
Yes, item is peer reviewed.
Scholarly level: 
Faculty/Staff
Final version published as: 

Karunarathna, C.B., Graham, J. perfectphyloR: An R package for reconstructing perfect phylogenies. BMC Bioinformatics 20, 729 (2019) DOI: 10.1186/s12859-019-3313-4.

Date created: 
2019-12-23
Keywords: 
Perfect phylogeny
Ancestry
Sequence
Trait-influencing variants
Abstract: 

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.

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.

 

Language: 
English
Document type: 
Article
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