perfectphyloR: An R Package For Reconstructing Perfect Phylogenies

Resource type
Date created
2019-12-23
Authors/Contributors
Abstract
BackgroundA 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.ResultsWe 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.ConclusionThe 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.BackgroundA 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.ResultsWe 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.ConclusionThe 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.
Document
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.
Publication title
BMC Bioinformatics
Document title
perfectphyloR: An R Package For Reconstructing Perfect Phylogenies
Date
2019
Volume
20
Issue
729
Publisher DOI
10.1186/s12859-019-3313-4
Copyright statement
Copyright is held by the author(s).
Scholarly level
Peer reviewed?
Yes
Language
Member of collection
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s12859-019-3313-4.pdf 902.29 KB